microorganisms in natural environments (soil)

ecosystem

interactions as a functional unit

how much of earth’s biomass is microbes

50%

species richness

total number of different species present

species abundance

the proportion of each species in an ecosystem

what is a guild

metabolically related microbial populations

what are microbial communities

sets of guilds that interact with macroorganisms and abiotic factors of the ecosystem

what is a microenvironment

the immediate environmental surroundings of a microbial cell or group of cells

soils particles contain many microenvironments

what defines the niche of a microbe

difference in the type and quantity of resources and the physiochemical conditions of a habitat

the niche determines growth

what differs between natural and lab environments

growth rate is lower than maximum growth rates

competition and cooperation occur between microbes and with higher organisms

what is biogeochemistry

the study of biologically mediated chemical transformations

what is a biogeochemical cycle

defines the transformations of a key element by biological and chemical agents

two types of soils

mineral soils and organic soils

mineral soils

derived from rock weathering and other inorganic materials

organic soils

derived from sedimentation in bogs and marshes

what are the components of soil

inorganic material (40%)

organic matter (5%)

air and water (50%)

living organisms

what is humus

dead plant material that is resistant to decomposition

keeps water and nutrients in the soil

where does most microbial growth take place

on the surfaces of soil particles

what is the most important factor influencing microbial activity

availability of water

how do the different soil types affect water retention

sand: water drains quickly

silt: retains water to the right extent

clay: water retained too well, soil becomes anoxic

what is the most important factor in subsurface environments

nutrient availability

what are bacteria and archaea responsible for in the soil

humus production

mineral release from soil

nutrient cycling

nitrogen fixation

rhizosphere

soil that surrounds plant roots and receive plant secretions

mychorrizae

association of fungi with plant roots

why can only some prokaryotes fix nitrogen

a lot of energy is required to break the triple bond between nitrogens

why is nitrogen fixation important

provides nutrients in the absence of fertilizer

how is nitrogen fixation catalyzed

by nitrogenase complex

ammonia is the final product

nitrogenase reductase is inhibited by the presence of oxygen

free living nitrogen fixers

widespread in soil, require organic matter to provide energy

ammonia can be used by plants

ex. clostridium, azotobacter

clostridium

free living nitrogen fixer

strict anaerobe

azotobacter

free living nitrogen fixer

strict aerobe

cyanobacteria as nitrogen fixers

only some species are capable

important role in nature

produce energy by oxygenic photosynthesis, oxygen is produced in the cell

where does nitrogen fixation occur in cyanobacteria

in heterocysts (anaerobic cells) which do not have PSII (no oxygen production)

heterocysts have a thick cell wall tthat slows down the diffusion of O2

regular cells provide heterocysts with pyruvate

symbiotic nitrogen fixers

legume plants and nitrogen fixing bacteria are mutualistic

rhizobium is best known bacteria

how does symbiotic nitrogen fixation work

legume roots are colonized by the bacteria and form root nodules where nitrogen fixation happens

how are nodules formed

1. recognition and attachment of bacterium to root hairs

2. excretion of nod factors by the bacterium

3. bacterial invasion of the root hair

4. travel to main root via the infection thread (made of cellulose)

5. formation of bacteroid state within plant cell

   1. continued plant and bacterial division, forming the mature root nodule

how are nodules regulated

oxygen levels are controlled by O2 binding protein leghemoglobin from the plant cells

bacteroids are a terminal state and cannot be shed

bacteroids use organic acids from photosynthesis in the plant

what are the implications for agriculture

plants need nitrogen

nitrate is more soluble than ammonium and easier for plants to uptake

nitrifying bacteria turn ammonia into nitrate

if soil is poorly drained and becomes waterlogged, soil becomes anaerobic, which promotes denitrification

anaerobic conditions promote sulfur and sulfate reduction which produce H2S which is toxic for plants