Term
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Definition
| study of biodiversity of microbes in nature; measure of activities & effects on microbes |
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| Microbial Ecology Organization Levels |
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Definition
| Populations, Guilds, Communities, Ecosystems |
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| Most elemental cycles run, controlled & moderated by microbes so not just geochemical cycles |
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Definition
| 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 |
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Definition
| separation of individual organisms from the mixed community |
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Definition
| 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 |
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| 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 |
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Definition
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 |
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Definition
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 |
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Definition
| 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 |
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| DAPI & Acridine Orange (AO) |
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Definition
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 |
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Term
| Viability Stains (viable counting) |
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Definition
| 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 |
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Term
| Fluorescent Antibody (Ab) Staining |
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Definition
| 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 |
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| Green Fluorescent Protein (GFP) |
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Definition
| 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 |
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Definition
| DNA or RNA complimentary to a sequence in a target gene or RNA molecule |
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| Fluorescent in situ hybridization (FISH) |
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Definition
| phylogenetic probes to find species-specific oligonucleotide signature sequences; highly specific & simple; multiple probing of single sample; culture not needed when this performed |
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Definition
| study unculturable organisms, determine morphology, abundance, microbial associations; probes allow for determination of species that couldn't be differentiated with just simple staining |
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Definition
| 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" |
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| FISH Chromosomal Painting |
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Definition
| 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) |
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Term
| In situ reverse transcriptase (RT) FISH |
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Definition
| 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 |
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| PCR & Microbial Community Analysis |
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Definition
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 |
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| Polymerase Chain Reaction (PCR) |
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Definition
| new process allows for no TAC polymerase inhibitors of PCR in community; able to amplify PCR |
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Definition
| 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 |
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| Microbial Activity Measurements |
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Definition
| 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 |
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Definition
| 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 |
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| FISH Microautoradiography (MAR) |
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Definition
| 14C or 35S used for short term; labeled sugars put on photographic plate; wherever radioactivity is concentrated shows what populations metabolizing |
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Definition
| Test physical parameters & compounds for specific metabolic activities; can tell where no O2 - orgs fermentative or anaerobic; can do w/o disturbing population |
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Definition
| 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 |
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| Carbon Isotopic Compositions |
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Definition
| Different substrates & their organic processes & result - how much carbon; CO2 fixed and fungi breaks down to release carbon into ecosystem |
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Term
| Populations, Guilds & Communities |
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Definition
| 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) |
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Definition
| 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 |
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Term
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Definition
| 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 |
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| Nutrient Levels & Growth Rate |
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Definition
| 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 |
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Definition
| neighbor gains access to nutrients faster, killing off competition; can also inhibit growth of others by releasing compounds as antibiotics (fungi) or bacteriosis |
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Definition
| work together instead of fighting; "Syntrophy"; close associations |
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Definition
| cooperation, eating together ("commensal") & working together ("Consortium") |
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Definition
| everyone works together metabolically so can share to attack particular substrate together, better |
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Term
| Terrestrial Environments (soil) |
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Definition
| Different horizons (layers of environments or microniches); most complex for microbes; each horizon has different nutrients, temps |
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Term
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Definition
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) |
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Term
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Definition
| 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 |
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| Terrestrial Environments (deep subsurface) |
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Definition
| Several to 1000+M; anaerobes that are sluggish chemoorganotrophs & chemolithotrophs (not a lot of organic available); no photosynthesis; divide only once every 100 years |
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Definition
| 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. |
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Definition
| 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 |
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Definition
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Definition
| Lower layer of water - provides nutrients |
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Definition
| highly mixed & high organic levels possible so lower O2 levels |
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| Biological Oxygen Demand (BOD) |
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Definition
| O2 consuming property of water; measures amt of organic material that can oxidize by microorgs; > BOD = > pollution & > org level; > carbon = < O2 |
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| Effect of high organic levels |
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Definition
| 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 |
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Definition
| Inshore - higher nutrient levels, high primary production, high heterotrophic activity, potentially low O2; inorganic materials allow heterotrophs to be vast |
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Definition
| open ocean depleted of photosynthesizers; high chlorophyll content inland, rivers |
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Definition
| limited inorganic nutrients, limited primary production; limited heterotrophs; O2 levels high. Cyanobacteria primary producers O2; 1/2 O2 we breathe from cyanobacteria |
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Term
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Definition
| 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) |
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Definition
| down to 3000M, no growth above 5000M |
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Definition
| 4000-6000m, optimum at 4000M |
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Definition
| 10000M, opt 7000-8000M, no growth <4000M |
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| Molecular effects of high pressure |
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Definition
| decrease binding capacity of enzymes, membrane process, use outer membrane porins to bind substrates; limited gene expression |
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Definition
| 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 |
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| What do the vents release? |
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Definition
| H2S, CO2, NH4+ (no organic material) |
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Term
| Vent invertebrate communities |
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Definition
| Sessile tubeworms and mollusks that live close to the vent; Receive C source (chemotrophic dependent), few predators; red parts (hemoglobin like) to attract nutrients |
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Term
| Chemolithotrophs of deep sea |
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Definition
| CO2 fixation from nutrients out of vents, tube worms have trophosomes that live inside tissue of worm; giant clams & methanotrophs that release CO2 |
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Term
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Definition
| prokaryotic cell symbionts in tube worms that use hemoglobins to bind O2 and H2S; Houses and delivers H2S and CO2 to chemoautotrophs |
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| Black smoker chimney worms |
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Definition
| chemolithotrophic bacteria grown on surface of worm bodies to hold nutrients; worms graze hairs & eat; not one homogenous population of bacteria |
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Term
| Higher temps for microbes |
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Definition
| in situ evidence for colonization, growth at 125-140oC; biological sulfate reduction at 130oC; ATP unstable at 150oC |
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Term
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Definition
| 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 |
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Definition
Main 2 types: CO2 fixation; Carbon mineralization (decomposition)
Other: Methanogenic archaea; Methylotrophs; Carbon monoxide metabolism |
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Definition
| 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 |
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Definition
| swamps, marshes, soils, protozoan endosymbionts, rumen, cows (burp 50L/day) |
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Definition
| digestive area of cow: find bacteria, protozoa, anaerobic fungi, microbial cells digested, microbial protein recovered; strict anaerobic fungi digests cellulose |
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| Chemoautotrophic benefits |
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Definition
| Maintain access to H2S and CO2 |
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Term
| Chemoautotrophy (sulfur cycle) |
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Definition
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| Sulfur-oxidizing chemoautotrophs |
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Definition
| H2S used as e- donor, bacteria fix CO2 to carbohydrate |
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Term
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Definition
| Presence of specific enzymes dictate metabolic capabilities/habitat distributions |
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Definition
| Chemical transformations by biological organisms; every element has own cycle, almost always moderated by microbes |
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| Purposes of biogeochemical cycles |
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Definition
| Converts one chemical form to another, maintains essential compounds in biosphere; leaching of ores (copper, gold); heavy metal transforms, biodegrade/biomediate toxins, etc |
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| Biogeochemical Cycles & Pseudomonas |
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Definition
| pseudomonas altered metabolically and put in toxic environment for cleanup; they don’t compete so eventually die out; fluorescence used to view colonies. |
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| Plant-Microorg Interactions |
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Definition
| 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) |
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Term
| Nitrogen Cycling (what is it required for) |
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Definition
| Protein synthesis; Nucleic acid synthesis; other cell components; Major reservoir of N2 is atmostphere |
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| What benefits are there with nitrogen fixation? |
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Definition
| Symbiotic relationships with plants (Rhizobium sp. and legumes) |
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| Non-symbiotic bacteria able to fix nitrogen |
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Definition
| Cyanobacteria; Azotobacter sp.; Clostridium sp. |
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Definition
| CO2 -> Organic carbon; CO2 is a major reservoir of carbon; CO2 fixation is done by Primary Producers (autotrophs) |
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| Carbon Mineralization (Decomposition) |
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Definition
| Organic carbon -> CO2; Sugar/protein/lipid decomposition; Organic carbon is often trapped in complex molecules (cellulose & lignin) |
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| Carbon mineralization (what happens?) |
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Definition
| Complex molecules not readily decomposed, so accumulation occurs; Many bacteria and fungi responsible for decomposition |
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Definition
| Anaerobic process done by methanogenic Archaea |
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| The sulfur cycle (2 types) |
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Definition
| Sulfur oxidation & reduction |
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Definition
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Definition
| Process called dissimilatory sulfate reduction |
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| What can SO4^2- be used for? |
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Definition
| As a sulfur source converted to -SH groups in proteins; This is called assimilatory reduction |
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Term
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Definition
| sum total of all organisms in specified environment |
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Definition
| portion of ecosystem suited to a specific population |
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| Eutrophic lake, eutrophication |
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Definition
| buildup of inorganic/organic material (nutrients) = eutrophication = fish die |
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Term
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Definition
| different oxygen levels, physical & chemical changes can change environment rapidly |
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| Aquatic habitats depend on what? |
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Definition
| rate of primary production (carbon) |
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| Primary producers of aquatic? |
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Definition
| phytoplankton & benthic algae |
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Term
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Definition
| restriction enzymes cut DNA at specific sequences; identifies higher level of phylogenetic tree (more general) |
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Term
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Definition
| separates down to the molecules of DNA, even if 1 base pair differs; identifies lower levels of tree (more specific) |
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Definition
| it is selective for isolation & different gradients; microbial diversity in artificial environments |
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Term
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Definition
ISRT: dyes nucleic acids; gene expression
FISH: dyes DNA, gene transcription |
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Term
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Definition
| experiment that uses intact tissue (no harm to sample bcz not individual cells) |
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Term
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Definition
| DNA staining, also use DAPI |
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Definition
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| gene transcription staining |
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Definition
| FISH chromosomal painting |
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Term
| Why are Gram (-) more dangerous as endotoxin? |
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Definition
| because Lipid A layer of LPS has toxins |
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