Microbial ecology exam 1

Define microbial ecology

Define microbial ecology

The study of how organisms interact in their environment

Role of Mycobacterium vaccae

-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

Louis Pasteur

• worked with fermentation and pasteurization

• Discovered the Germ Theory of Disease

• First microbial ecologist

Robert Koch

• discovered that bacillus causes cholera and anthrax

• Developed pure culture paradigm

• Introduced use of agar media for pure culturing

Sergei Winogradsky

• isolated nitrafying bacteria

• described oxidation of H2S and Fe2+

• coined chemoautotrophy

• founder of soil microbiology

Martinus Beijerinck

• 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

J. G. Lipman

• established soil microbiology in the us

• Established department of soil chemistry and bacteriology

• Developed book: Bacteria in Relation to Country Life

Albert Bernard Frank

• botanist and mycologist

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

• First to show that some fungi are symbiotic

Selman Waksman

• discovered streptomycin and neomycin

Geosmin

• Earthy flavor and aroma in soil

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

Alexander Fleming

• discovered lysozyme

• Discovered penicillin

Streptomyces spp.

• filamentous bacteria

• Phylum: Actinobacteria

• Produces spores for reproduction

• Responsible for earthy odor of soils

Problems with penicillin

• unstable at low and high pH

• Only produced in small quantities even by prolific cultures

• Fungus only grows well in soil media

Dennis Parkinson

• Importance of microbial-microfaunal interactions in soil processes

• Fungal ecology of root zone

Carl Woese

Discovered the third domain of life, archaea

what is soil?

• 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

what is the composition of soil?

• 25% water

• 25% air

• 45% minerals

• 5% organic matter

what are clays?

• polysilicate complexes of silicon and aluminum

• derived from the weathering of other rocks

• sheet-like complexes that have a negative charge

structure of soils

• 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

what are the four major types of soil?

• 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)

what are the 3 major soil horizons?

• surface horizon (A)

• subsoil (B)

• substratum (C)

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

the three layers of the organic layer

• 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)

topsoil (A horizon)

• 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

subsoil (B horizon)

• rich in minerals that leach from the A horizon

• lower microbial activity

• water storage for plants

Parent material (C horizon)

• material from which soil is formed

• can be very deep if buried

name the different soil types found in America

• aridisols

• entisols

• mollisols

• utisols

• alfisols

• inceptisols

Aridisols

• 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

Entisols

• 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

Mollisols

• 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

Utisols

• 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

Alfisols

• 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

Inceptisols

• 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

all soils have ____ that determines their ability to capture and retain moisture

pore structure

bulk density

• 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

the weight of material taking up volume determines _____

bulk density

what aspects of soils are influenced by soil structure?

• water filtration

• aeration

• microbial activity

• carbon sequestration levels

• root growth

• nutrient retention and conversions

for most loamy soils, __% to __% of their volume are pores and only __% of their pores have to be air-filled to be aerobic

• 50

• 60

• 10

(T/F) the soil atmosphere has a higher concentration of CO2 than the regular atmosphere

true

sources of higher CO2

• microbial respiration

• root respiration

• microfaunal respiration

the movement of gases in soil are dependent on:

• size of soil pores

• amount of pores that are water filled

• solubility of gas in water

(T/F) soils are very heterogenous in their atmosphere based upon their structure

true

if soils are too wet, they quickly become _____ due to the slow diffusion of O2 into the soil structure and the solubility of O2 in water

anaerobic

unsaturated soil

the pores do not contain much water

saturated soil

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

flooded soil

water is filling the pores and vegetation

field capacity

the amount of available water for plant growth

wilting point

no more water is available for plants

gravimetric water content

• 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

permanent wilting point

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

water potential

• 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)

gravitational potential

• the water pulled from soil by gravity

• not important unless the soils have very large pores

matric potential

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

• the major determining factor

how to measure soil matric potential

• 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

(T/F) water potential is measured as a positive value - amount of force needed to push water from the pores

false

what is the water potential of pure water?

0.00 MPa

what is the range of WP that bacteria and fungi can be active in soil?

• for bacteria: -0.03 to -0.10 MPa

• fungi: -1.5 to -8.0 MPa

what influences the size and densities of soil pores?

• 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

what limits microbial growth?

• 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

(T/F) bacteria are protein rich and require a high amount of nitrogen

true

fungi are _rich and have a high _ percentage

• lipid

• carbohydrate

humans have a macromolecule percentage similar to which type organism?

fungi

what do the carbon:nitrogen ratios indicate?

the capacity of microbes to use different types of carbon sources

what are the carbon:nitrogen ratios of bacteria, fungi, humans, wheat straw, and wood?

• bacteria: 3:1 - 5:1

• fungi: 15:1 - 20:1

• humans: 25:1

• wheat straw: 50:1

• wood: 200:1 - 400:1

autotrophs

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

heterotrophs

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

categories of carbon acquisition

• saprophites: use dead organic matter

• pathogens: colonize living host

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

phototroph

• use sunlight to generate ATP (photosynthetic bacteria)

chemotroph

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

photoautotroph

use light energy and inorganic carbon to produce organic materials

• photosynthetic bacteria

  -cyanobacteria

  -no fungi

oxygenic photosynthesis

obtain reducing power from splitting of water

photoheterotroph

• 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

chemoautotroph

• 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

chemoheterotroph

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

• all fungi

• most bacteria

the two types of controls on a population and community

• 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

(T/F) viruses are the most abundant biological entities

true

virus characteristics

• 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

what are the two basic types of replication strategies for viruses?

• lytic phase:

  -virulent viruses

• lysogenic phase:

  -temperate phages

  -can be induced to become lytic

the two ways to quantify viruses in natural environments

• plaque assay

  -underestimates quantity due to issues of bacterial culturability

• epifluorescence microscopy

(T/F) virulent viruses have a larger effect in shaping host populations over longer periods of time

false; temperate viruses

how can we estimate the number of lysogenic bacteria in a sample?

• 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

microbial viruses control host densities via _____

density-dependent lytic-predator dynamics

virus-like particles are ___ abundant at __ host densities

• less

• high

temperate cycles become ___ abundant at ___ host densities

• more

• higher

as viral and host densities ____, lysogeny resistance to superinfections become important

increase

(T/F) lysogeny can reduce predation by protists

true

the ___ in lysogeny can lead to ___ nutrient cycling and lower ecosystem dynamics

• increase

• reduced

(T/F) the host range for viruses is limited because the viruses infect its host by highly specific mechanisms

true

viral lysis

• 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

viruses and their role in nutrient cycling

• 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

mycoviruses

• 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

free mycoviruses are not numerous because:

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

(T/F) the chitin cell wall of fungi is one defense against infection by free mycoviruses, but it can not explain completely why fungi are resistant

true

bacteria can take genes from other cells through which three mechanisms?

• transformation

• conjugation

• transduction

(T/F) infection by a virus can lead to new pathways that involve the conversion of non-pathogenic strains of bacteria to pathogenic strains

true

coliphages

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

what is an ecosystem?

• 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

what are some examples of how the biotic and abiotic environment interact?

• temperature patterns

• annual rainfall and weather patterns

• soil type

• wind, relative humidity

• nutrient availability and amounts

how do we study ecosystems?

• look at primary productivity

• examine trophic dynamics

• examine carbon flow (energy)

• examine nutrient dynamics

what are crucial ecosystem services?

• 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

what does the simplest functional terrestrial ecosystem consist of?

• water

• soil

• primary producers

• minerals

• decomposers

• air

• energy (sunlight)