Microbial ecology exam 1

The study of how organisms interact in their environment

-activates immune cells which release cytokines

- increases serotonin production in mice

-by inhaling it while working outside, you get elevated serotonin levels and feel better

• worked with fermentation and pasteurization

• Discovered the Germ Theory of Disease

• First microbial ecologist

• discovered that bacillus causes cholera and anthrax

• Developed pure culture paradigm

• Introduced use of agar media for pure culturing

• isolated nitrafying bacteria

• described oxidation of H2S and Fe2+

• coined chemoautotrophy

• founder of soil microbiology

• founder of the Dutch deft school of microbiology

• Approached microbiology through the study of microbial ecology

• 1st to isolate nitrogen fixing bacteria and isolated sulfur reducing bacteria

• Coined microbial ubiquity

• Recognized bacteria of major contribution to element transformation

• established soil microbiology in the us

• Established department of soil chemistry and bacteriology

• Developed book: Bacteria in Relation to Country Life

• botanist and mycologist

• Coined term mycorrhizae to describe symbiotic relationship between trees and turtles

• First to show that some fungi are symbiotic

• discovered streptomycin and neomycin

• Earthy flavor and aroma in soil

• Ex. Source of strong scent from rain; gives beets earthy flavor

• discovered lysozyme

• Discovered penicillin

• filamentous bacteria

• Phylum: Actinobacteria

• Produces spores for reproduction

• Responsible for earthy odor of soils

• unstable at low and high pH

• Only produced in small quantities even by prolific cultures

• Fungus only grows well in soil media

• Importance of microbial-microfaunal interactions in soil processes

• Fungal ecology of root zone

Discovered the third domain of life, archaea

• organic materials of various types and levels of decomposition

• living microbes, plant roots, and soil animals (protozoans, mites, nematodes)

• water

• dissolved minerals

• inorganic minerals and materials (sand, silt, clay)

• atmosphere of various gases

• 25% water

• 25% air

• 45% minerals

• 5% organic matter

• polysilicate complexes of silicon and aluminum

• derived from the weathering of other rocks

• sheet-like complexes that have a negative charge

• includes the formation of clay-organic material; microbe complexes that provide the matrix that is the soil

• composed of a combination of microaggregates and macroaggregates

• silt loam (15% sand, 15% clay, 70% silt)

• sandy loam (15% clay, 20% silt, 65% sand)

• clay (15% silt, 15% sand, 70% clay)

• loam (20% clay, 40% silt, 40% sand)

• surface horizon (A)

• subsoil (B)

• substratum (C)

• other types: organic horizon (O), master horizon (E), and hard bedrock (R)

• litter layer: new plant material being deposited

• fermented layer: fungi and bacteria decompose plant material

• humus layer: organic matter that has been acted upon by microbes and converted to long-term carbon storage (important for nutrient storage)

• composed of mainly minerals from parent material with organic matter incorporated; good microbial activity

• may be up to 10 in. deep

• very productive soils

• in grasslands

• bottom can be eluviated (leached out) with the loss of iron oxides and aluminum oxides

• rich in minerals that leach from the A horizon

• lower microbial activity

• water storage for plants

• material from which soil is formed

• can be very deep if buried

• aridisols

• entisols

• mollisols

• utisols

• alfisols

• inceptisols

• too dry for growth of mesophytic plants

• accumulate gypsum, salt, and calcium carbonate (easily leached from more humid environments)

• common in deserts

• 12% of earth’s ice-free land surface

• little to no evidence of pedagonic horizon development

• in areas of recently deposited parent material or areas where erosion rates are faster than the development of soil

• in dunes, steep slopes and flood plains

• 16% of ice-free land surface

• dark-colored surface horizon relatively high in content of organic matter

• base-rich throughout, quite fertile

• under grass in climates with seasonal moisture deficit

• dry prairie soils; soils of dry climates that are hot during the summer

• 7% of ice-free land surface

• in humid areas

• acid soils; nutrients concentrated in upper few inches

• formed from intense weathering and leaching processes that result in clay-enriched subsoil dominated by mineral such as quartz, kaolinite, and iron oxides

• moderately low capacity to retain additions of limes and fertilizer

• make up about 8% of earth’s ice-free land surface

• occur in semi-arid to moist areas

• formed from weathering processes that leach clay and other constituents out of the surface layer and into the subsoil, where they can hold and supply moisture and nutrients to plants

• formed primarily under forest or mixed vegetative cover and are productive for most crops

• make up about 10% of earth’s ice-free land surface

• semi-arid to humid environments with moderate soil weathering and development

• occur in diverse climates and have wide variety of characteristics

• 17% of earth’s ice-free land surface

pore structure

• the total space occupied by solids and pore spaces

• influenced by the amount of soil organic matter and rocky substrates

• influences soil moisture storage and microbial activity

  -soils with high bulk density have large pores

  -soils with low bulk density have small pores

bulk density

• water filtration

• aeration

• microbial activity

• carbon sequestration levels

• root growth

• nutrient retention and conversions

• 50

• 60

• 10

true

• microbial respiration

• root respiration

• microfaunal respiration

• size of soil pores

• amount of pores that are water filled

• solubility of gas in water

true

anaerobic

the pores do not contain much water

water is stored in the pores; the pores are filled and the gravitational water is lost

water is filling the pores and vegetation

the amount of available water for plant growth

no more water is available for plants

• the amount of water held in the soil pores against the pull of gravity

• the larger the pores, the less water the soil can hold

• the smaller the pores, the more water the soil can hold

  -however, as pores get smaller, it is harder for plant microbes to use that water

the water content of the soil at which plants cannot extract any water and the plant does not recover from wilting

• the amount of soil water available to do biological work

• measured as the force necessary to push water from the pores

• WP= matric potential (MP) + gravitational potential (GP) + osmotic potential (OP)

• the water pulled from soil by gravity

• not important unless the soils have very large pores

• the amount of energy needed to remove water from soil pores for biological activity by diffusion

• the major determining factor

• saturate soils to field capacity

• add a pressure to see how much water is forced out

• keep adding pressure until you cannot extract any more water

• record water weight vs pressure added

• matric potential is measure as a negative value in MPa

false

0.00 MPa

• for bacteria: -0.03 to -0.10 MPa

• fungi: -1.5 to -8.0 MPa

• the amount of sand, silt and clay

• the amount of soil organic matter

• the amount of soil disturbance

• the level of microbial activity creating soil organic matter

• temperature dynamics

• oxygen levels

• temporal and spatial variability of carbon

• quality of carbon

• temporal and spatial variability of ammonium and nitrate

• concentration of iron

• concentration of phosphorus

• pH

true

• lipid

• carbohydrate

fungi

the capacity of microbes to use different types of carbon sources

• bacteria: 3:1 - 5:1

• fungi: 15:1 - 20:1

• humans: 25:1

• wheat straw: 50:1

• wood: 200:1 - 400:1

fix carbon dioxide onto carbohydrates (plants, algae, and some bacteria - cyanobacteria)

use previously fixed carbon for growth (most bacteria and all fungi)

• saprophites: use dead organic matter

• pathogens: colonize living host

• symbiotic: obtain carbon from living hosts and provide benefits in return (Mycorrhizal fungi, Rhizobium, Frankia)

• use sunlight to generate ATP (photosynthetic bacteria)

use oxidation/reduction or organic compounds (inorganic compounds for energy generation)

use light energy and inorganic carbon to produce organic materials

• photosynthetic bacteria

  -cyanobacteria

  -no fungi

obtain reducing power from splitting of water

• use sunlight for energy

• purple/green nonsulfur bacteria

• strict anaerobes

• cannot use carbon dioxide as sole carbon source; use some organic molecules for growth

• use inorganic compounds for reducing power

• synthesize all organic compounds from carbon dioxide

• use inorganic compounds for reducing power

• found in soils, deep-sea thermal vents, hot springs

• nitrifying bacteria crucial for soil

• no fungi

• obtain carbon from previously fixed carbon and energy from oxidation/reduction of the organic carbon

• all fungi

• most bacteria

• bottom-up: limitations placed by resource availbility of carbon source, nitrogen, phosphorus, or habitat availability within a landscape

• top-down: limitations place by factors controlling death, such as predation, disease or reoccurring disturbances, such as wave action or fires

true

• must infect a host in order to replicate

• viruses use top-down control

• very simple, consist of only NA surrounded by a protein coat, capsid, and for some viruses by membranes and tails

• have several types of morphologies

• some of their shapes are determined by how capsid protein subunits are arranged to house the viral genome

• lytic phase:

  -virulent viruses

• lysogenic phase:

  -temperate phages

  -can be induced to become lytic

• plaque assay

  -underestimates quantity due to issues of bacterial culturability

• epifluorescence microscopy

false; temperate viruses

• count viruses before and after the addition of mitomycin C or by exposure to UV light or both to induce the switch from lysogenic to lytic

• an increase in viruses after the induction treatment indicates the presence of inducible prophages within the microbial community and is a proxy for the number of temperate viruses in that habitat

density-dependent lytic-predator dynamics

• less

• high

• more

• higher

increase

true

• increase

• reduced

true

• viral lysis releases dissolved and particulate organic material because of the dependence of the virus on a functioning host

• lysis by the virus releases the host’s cellular contents into the environment with little oxidation or mineralization

• in soils, the released cellular contents may adsorb into surfaces

• whereas, in aquatic habitats they may become part of the dissolved organic material (DOM) pool

• viral shunt: the production of DOM by viral lysis and its subsequent use by microbes

• in marine ecosystems, viruses play a significant role in the cycling of food molecules

  -marine viruses infect most phytoplankton, releasing their minerals in the upper water, where they are available for other phototrophs

• viruses play an important role in carbon balance

• viruses that infect fungi

• can be transmitted vertically via fungal spores and horizontally (hyphae anastonosis)

  -the horizontal mechanism involves the fusion of two fungal hyphae resulting in the exchange of genetic and cytoplasm material

• don’t have to lyse cells in order to complete replication cycle

• can affect the physiology of fungi

they can be transmitted from one fungus to another without being released as a free particle into the external environment

true

• transformation

• conjugation

• transduction

true

• gut bacteriophages that modulate human digestion, the immune system, and mental health

• specific location

• interaction of all the organisms that exist and move in that location

• ecosystems can be scale dependent

• includes the abiotic environment

• all of the attendant ecosystem services that exist as a consequence of interactions with the biotic and abiotic components of the environment

• temperature patterns

• annual rainfall and weather patterns

• soil type

• wind, relative humidity

• nutrient availability and amounts

• look at primary productivity

• examine trophic dynamics

• examine carbon flow (energy)

• examine nutrient dynamics

• production of O2 from photosynthesis

• fixation of CO2 into plant biomass

• production of energy to support the environment

• decomposition

• nitrogen cycling

• terrestrial water capture

• clean-up of human waste

• water

• soil

• primary producers

• minerals

• decomposers

• air

• energy (sunlight)