question

Microbial Ecology

answer

study of biodiversity of microbes in nature; measure of activities & effects on microbes

question

Microbial Ecology Organization Levels

answer

Populations, Guilds, Communities, Ecosystems

question

Biogeochemical Cycles

answer

Most elemental cycles run, controlled & moderated by microbes so not just geochemical cycles

question

Enrichment & Isolation

answer

Not just relying on med microbiology - study microbes out in environment; enrichment highly selective & appropriate inoculum used - can add Organic N, atmospheric N, heterotrophic populations grow, nitrogen-fixing bacteria appear & not overgrown

question

Isolation

answer

separation of individual organisms from the mixed community

question

Enrichment cultures

answer

select for desired organisms through manipulation of medium and incubation conditions; easy to tell bacteria is there, hard to prove that it's not there

question

Winogradsky column

answer

miniature ecosystem w/o homogenous mixture; serves as long-term source of bacteria for enrichment cultures; soil, water ; light; each tube has different environment for different activities

question

Enrichment bias

answer

Microorganisms cultured in lab are frequently only minor compoennts of the natural microbial ecosystem
in lab only able to provide beneficial environments for a few types of microorganims, therefore only these species are benefit

question

Pure cultures

answer

w/ enrichment ; isolation ; manipulation; contain a single kind of microorganism (can be obtained by streak plate, agar dilution or liquid dilution)
they are clones of cells started from an individual cell

question

Fluorescent Staining

answer

Used for enumeration ; mainly for nucleic acids or DNA; view w/ fluorescent microscope; Might have some UV damage; 3 Types: DNA-binding stains, Acridine Orange (orange or green), DAPI

question

DAPI ; Acridine Orange (AO)

answer

Different staining methods:
DAPI and AO fluoresce under UV light, are nonspecific and stain nucleic acids
DAPI stains bright blue; AO stains orange or greenish-orange
*cannot differentiate between live and cells

question

Viability Stains (viable counting)

answer

can differentiate between live and dead cells bcz two dyes are used; based on integrity cell membrane (not intact in dead cells); green cells alive ; red dead

question

Fluorescent Antibody (Ab) Staining

answer

Monochrome staining; can be used as a cell tag; highly specific for the molecule recognized by Ab; used to identify any type of cell for specific Ab; making antibodies is time consuming and expensive

question

Green Fluorescent Protein (GFP)

answer

genetically engineered into cells to track bacteria, if always expressed; can act as a reporter gene, if fused to a promoter of interest; can use fluorescence to see how much bacteria still living

question

Nucleic acid probe

answer

DNA or RNA complimentary to a sequence in a target gene or RNA molecule

question

Fluorescent in situ hybridization (FISH)

answer

phylogenetic probes to find species-specific oligonucleotide signature sequences; highly specific ; simple; multiple probing of single sample; culture not needed when this performed

question

FISH Community Analysis

answer

study unculturable organisms, determine morphology, abundance, microbial associations; probes allow for determination of species that couldn't be differentiated with just simple staining

question

Multiple FISH Probes

answer

Not based on 16s taxonomy; based on physiology & nitrogen cycle; can view different activities of different organisms with supporting metabolisms with different color probes for that specific sig sequence ("Multiplexing"); activities can work off of or support each other in "Consortium"

question

FISH Chromosomal Painting

answer

identify specific genes; locate, count specific metabolic populations; can search for whatever gene you require; can determine specific gene expression & transcription activites by different dyes, physiology & neighboring organisms; find out who's doing what (genes turned on)

question

In situ reverse transcriptase (RT) FISH

answer

Locates specific genes ; detects expression for those genes; needed when RNA is present, not DNA, so RT needed for complementary DNA; can run multiple tests - see specific genes turned on/off

question

PCR ; Microbial Community Analysis

answer

Can determine candidate name for unknown genes until bug isolated ; description correlated
Path 1: Extract total community DNA, amplify with PCR ; fluorescent tagged primers; put on T-RFLP gel; excise bands ; clone 16s rRNA genes; sequence; generate tree; Path 2: extract, amplify with general/restrictive primers (bacteria or endospore-specific); use DGGE gel, excise bands; sequence; generate tree

question

Polymerase Chain Reaction (PCR)

answer

new process allows for no TAC polymerase inhibitors of PCR in community; able to amplify PCR

question

Environmental Genomics

answer

Phylogenetic Tree for single genes or total gene pool of community; can identify ; link to phenotypes; Path 1: amplify single gene ; sequence, generate tree; Path 2: restriction enzymes digest all DNA then shotgun sequence or seq directly (w/o cloning); get partial genomes ; can discover new genes, link to phylotypes

question

Microbial Activity Measurements

answer

Microcosms - take sample of soil to lab w/o disturbing environment; label w/ different macromolecules based on metabolic processes wanted; track where things are going, what happens to substrate; Two Types: Radioisotopes ; Microelectrodes

question

MAM Types

answer

Radioisotopes: high sensitivity, turnover rates, fate of substrate ; killed cell control; Microelectrodes: micromanipulator, microbial mats ; multiple electrodes; can look at physical aspects like O2 tension, pH, H2S concentration; can multiplex and look at multiple states at once

question

FISH Microautoradiography (MAR)

answer

14C or 35S used for short term; labeled sugars put on photographic plate; wherever radioactivity is concentrated shows what populations metabolizing

question

Microelectrodes

answer

Test physical parameters ; compounds for specific metabolic activities; can tell where no O2 - orgs fermentative or anaerobic; can do w/o disturbing population

question

MAM Stable Isotopes

answer

Biogeochemical cycles ; food chains: 12C, 13C, etc - stable isotopes that hang around for awhile - used for biological processes; enzymes very selective and will favor one isotope over another; fractionates isotopes by selectively enriching 12CO2 to 12C and diminishes 13CO2 to 13C; shows how much enzymes moderate organisms ; fixes carbon

question

Carbon Isotopic Compositions

answer

Different substrates ; their organic processes ; result - how much carbon; CO2 fixed and fungi breaks down to release carbon into ecosystem

question

Populations, Guilds ; Communities

answer

Community 1: photic zone (oxygenic phototrophs), Comm 2: oxic (O2 loving ; facultative); Comm 3 (sediments): Anoxic (ferm, anaerobic); Guild 1: methanogenic or homoacetogenic bacteria; Guild 2: sulfate- or sulfur-reducing bacteria; Guild 3: denitrifying or ferric iron-reducing bacteria: Guild 4: ferm bacteria (ferm sugars, acids, etc)

question

Guilds

answer

Metabolically related populations of microbes that work together to ferment, depending on environment; each guild makes similar product in own process; each element has own guild to perform their own process; unique to microbial ecology

question

Microenvironments

answer

Prime niche; spatially very small; physical or chemical conditions change rapidly; heterogenous; environments change physiology ; can change (increase/low pH, etc) from physical or chemical; different numbers show levels of O2 for each niche

question

Nutrient Levels ; Growth Rate

answer

Feast or famine - when things get bad, organisms sacrifice self to help rest of population; happens when nutrients low or distribution not uniform; competition; no periods of optimal growth; when nutrients high, metabolism increases exponentially; organisms grow quickly ; die quickly

question

Competition

answer

neighbor gains access to nutrients faster, killing off competition; can also inhibit growth of others by releasing compounds as antibiotics (fungi) or bacteriosis

question

Cooperation

answer

work together instead of fighting; "Syntrophy"; close associations

question

Syntrophy

answer

cooperation, eating together ("commensal") ; working together ("Consortium")

question

Consortium

answer

everyone works together metabolically so can share to attack particular substrate together, better

question

Terrestrial Environments (soil)

answer

Different horizons (layers of environments or microniches); most complex for microbes; each horizon has different nutrients, temps

question

Terrestrial Horizons

answer

O: undecomposed plant materials
A: surface soil (high in organic, dark, tilled for agriculture; plants ; large #'s microbes grow)
B: subsoil (minerals, humus, leached from soil; little organic; low microbial activity)
C: soil base (directly from underlying bedrock; microbial very, very low)

question

Soil Aggregate

answer

Microcolonies form on different soil particulates held together by minerals from organisms or fungi w/ EC polysacch "glue"; each mineral (clay, water, quartz) has different surface properties for different microcolonies to grow & flourish

question

Terrestrial Environments (deep subsurface)

answer

Several to 1000+M; anaerobes that are sluggish chemoorganotrophs & chemolithotrophs (not a lot of organic available); no photosynthesis; divide only once every 100 years

question

Aquatic Habitats

answer

Diverse (oceans, marshes, etc); phototrophic microorganisms are primary producers & drive carbon into ecosystem; phytoplankton bottom dwellers; benthic algae; biologic activity depends on rate of primary production.

question

Aquatic O2 Relationships

answer

O2 limited solubility in H2O; O2 depletion when heterotrophs use up oxygen; Stratification of deep lakes: epilimnion & hypolimnion; when frozen, hypo no longer supports water so crashes down below for nutrients & support; might have high levels of organic matter from leaves falling, etc

question

Epilimnion

answer

Upper layer of water

question

Hypolimnion

answer

Lower layer of water - provides nutrients

question

Aquatic - Rivers

answer

highly mixed & high organic levels possible so lower O2 levels

question

Biological Oxygen Demand (BOD)

answer

O2 consuming property of water; measures amt of organic material that can oxidize by microorgs; > BOD = > pollution & > org level; > carbon = < O2

question

Effect of high organic levels

answer

when point source hits, organic carbon and BOD increases while O2 greatly decreases; eventually, carbon taken up and BOD decreases or bacteria moves; levels normalize, move up and down

question

Marine Environment

answer

Inshore - higher nutrient levels, high primary production, high heterotrophic activity, potentially low O2; inorganic materials allow heterotrophs to be vast

question

Chlorophyll Distribution

answer

open ocean depleted of photosynthesizers; high chlorophyll content inland, rivers

question

Open Oceans

answer

limited inorganic nutrients, limited primary production; limited heterotrophs; O2 levels high. Cyanobacteria primary producers O2; 1/2 O2 we breathe from cyanobacteria

question

Deep Sea

answer

Photic zone 0-300M; biologically active lower; Deep >1000M; water relatively inactive biologically; low temp & nutrients, high pressure; physiologically separated microbes based on pressure (baro)

question

Barotolerant

answer

down to 3000M, no growth above 5000M

question

Barophilic

answer

4000-6000m, optimum at 4000M

question

Extreme Barophiles

answer

10000M, opt 7000-8000M, no growth <4000M

question

Molecular effects of high pressure

answer

decrease binding capacity of enzymes, membrane process, use outer membrane porins to bind substrates; limited gene expression

question

Hydrothermal vent

answer

volcanic environment at ocean bottom (deep sea vents); black smoker chimneys very hot, metal sulfides & hydrothermal gradients; metabolism occurs in surrounding areas of sea mounts

question

What do the vents release?

answer

H2S, CO2, NH4+ (no organic material)

question

Vent invertebrate communities

answer

Sessile tubeworms and mollusks that live close to the vent; Receive C source (chemotrophic dependent), few predators; red parts (hemoglobin like) to attract nutrients

question

Chemolithotrophs of deep sea

answer

CO2 fixation from nutrients out of vents, tube worms have trophosomes that live inside tissue of worm; giant clams & methanotrophs that release CO2

question

Trophosome

answer

prokaryotic cell symbionts in tube worms that use hemoglobins to bind O2 and H2S; Houses and delivers H2S and CO2 to chemoautotrophs

question

Black smoker chimney worms

answer

chemolithotrophic bacteria grown on surface of worm bodies to hold nutrients; worms graze hairs & eat; not one homogenous population of bacteria

question

Higher temps for microbes

answer

in situ evidence for colonization, growth at 125-140oC; biological sulfate reduction at 130oC; ATP unstable at 150oC

question

Carbon cycle

answer

carbon reservoirs in land/living plants; a lot of carbon in humus; CO2 transfers; photosynthesis (terrestrial, aquatic); decomp produces methane (CH4) & CO2; both organic aerobic & anaerobic ferments to release carbon back into atmosphere

question

Carbon Cycle 2 types

answer

Main 2 types: CO2 fixation; Carbon mineralization (decomposition)
Other: Methanogenic archaea; Methylotrophs; Carbon monoxide metabolism

question

Humus

answer

mix of phenolic compounds that enzymatically bind together, like a sponge in soil - it holds majority of carbon; microbes must go through humus to get carbon

question

methanogenic habits

answer

swamps, marshes, soils, protozoan endosymbionts, rumen, cows (burp 50L/day)

question

Rumen

answer

digestive area of cow: find bacteria, protozoa, anaerobic fungi, microbial cells digested, microbial protein recovered; strict anaerobic fungi digests cellulose

question

Chemoautotrophic benefits

answer

Maintain access to H2S and CO2

question

Chemoautotrophy (sulfur cycle)

answer

H2S = H+ donor for ETC

question

Sulfur-oxidizing chemoautotrophs

answer

H2S used as e- donor, bacteria fix CO2 to carbohydrate

question

Metabolic Diversity

answer

Presence of specific enzymes dictate metabolic capabilities/habitat distributions

question

Biogeochemical cycles

answer

Chemical transformations by biological organisms; every element has own cycle, almost always moderated by microbes

question

Purposes of biogeochemical cycles

answer

Converts one chemical form to another, maintains essential compounds in biosphere; leaching of ores (copper, gold); heavy metal transforms, biodegrade/biomediate toxins, etc

question

Biogeochemical Cycles & Pseudomonas

answer

pseudomonas altered metabolically and put in toxic environment for cleanup; they don’t compete so eventually die out; fluorescence used to view colonies.

question

Plant-Microorg Interactions

answer

Ways to put Nitrogen into ecosystem; plants (legumes/nonlegumes), Gram (-), N2 fixing bacteria, root/stem nodule bacteria; Plants reliable - bacteria nutrient rich & gets N2 from plant; high species specificity (only 1 species per plant)

question

Nitrogen Cycling (what is it required for)

answer

Protein synthesis; Nucleic acid synthesis; other cell components; Major reservoir of N2 is atmostphere

question

What benefits are there with nitrogen fixation?

answer

Symbiotic relationships with plants (Rhizobium sp. and legumes)

question

Non-symbiotic bacteria able to fix nitrogen

answer

Cyanobacteria; Azotobacter sp.; Clostridium sp.

question

CO2 fixation

answer

CO2 -> Organic carbon; CO2 is a major reservoir of carbon; CO2 fixation is done by Primary Producers (autotrophs)

question

Carbon Mineralization (Decomposition)

answer

Organic carbon -> CO2; Sugar/protein/lipid decomposition; Organic carbon is often trapped in complex molecules (cellulose & lignin)

question

Carbon mineralization (what happens?)

answer

Complex molecules not readily decomposed, so accumulation occurs; Many bacteria and fungi responsible for decomposition

question

CH4 production from CO2

answer

Anaerobic process done by methanogenic Archaea

question

The sulfur cycle (2 types)

answer

Sulfur oxidation & reduction

question

Sulfur oxidation

answer

elemental sulfur

question

Sulfur Reduction

answer

Process called dissimilatory sulfate reduction

question

What can SO4^2- be used for?

answer

As a sulfur source converted to -SH groups in proteins; This is called assimilatory reduction

question

Ecosystem

answer

sum total of all organisms in specified environment

question

Habitat

answer

portion of ecosystem suited to a specific population

question

Eutrophic lake, eutrophication

answer

buildup of inorganic/organic material (nutrients) = eutrophication = fish die

question

Microenvironments

answer

different oxygen levels, physical & chemical changes can change environment rapidly

question

Aquatic habitats depend on what?

answer

rate of primary production (carbon)

question

Primary producers of aquatic?

answer

phytoplankton & benthic algae

question

PCR gel T-RLFP

answer

restriction enzymes cut DNA at specific sequences; identifies higher level of phylogenetic tree (more general)

question

PCR gel DGGE

answer

separates down to the molecules of DNA, even if 1 base pair differs; identifies lower levels of tree (more specific)

question

Winogradsky column

answer

it is selective for isolation & different gradients; microbial diversity in artificial environments

question

Chromosomal staining

answer

ISRT: dyes nucleic acids; gene expression
FISH: dyes DNA, gene transcription

question

In situ?

answer

experiment that uses intact tissue (no harm to sample bcz not individual cells)

question

Acridine Orange

answer

DNA staining, also use DAPI

question

gene expression staining

answer

ISRT

question

gene transcription staining

answer

FISH chromosomal painting

question

Why are Gram (-) more dangerous as endotoxin?

answer

because Lipid A layer of LPS has toxins

Microbial Ecology Test Questions – Flashcards

Unlock all answers in this set

Haven't found what you were looking for?

Search for samples, answers to your questions and flashcards