Micros- Chapter 22/23

biodiversity & microbial activity

bacteria that derived from a single cell

Populations that are metabolic related

set of guilds

Communities of organisms and their natural environment

Biological and chemically mediated chemical transformation of elements

"cycling of elements'

typically by oxidation-reduction rxn

growth and function at optimal levels, habitat,

Physical habitat -determines the niche

• Mutualism: + / +
• Commensalism: + / 0
• Ammensalism: 0 / -
• Parasitism: + / -
• Symbiosis: -share the same ecosystem

• Ubiquity - Biodiversity
• Abundance
• Metabolic Power - microbial activity

• 1. streak - drag to a single colony
• 2. agar shake - molton agar, double layer- colonies embedded in agar.
• 3. Liquid Dilution - serially dilute until no growth. also called MPN

• Most Probable Number analysis
• a repeat dilution series
• used for estimating the number of microorganisms in foods, waster, and other samples

• 1. microscopy - gram stain
• 2. observation of colony characteristics on plate or shake tubes
• 3. growth in media in which the culture grows poorly but contaminates grow well.

• 1. microorganisms will change characteristics to benefit them in a lab setting
• ex - pathogens lose virilence - may have different antigens
• 2. microbial communities are too small (3mm)

• algae & cyanobacteria
• purple non sulfur bacteria
• sulfur chemolithotrophs
• purple & green sulfur bacteria
• Anoxic decomposition & sulfate reduction

gradient: O₂ to H₂S & light gradient

• 1. faster growht than natural habitat because of feeding all the good stuff (food scarce in nature)
• 2. slower growth, microorganism may need another factor that is unknown.

• 1. PCR and DGGE
• 2. Metagenomics
• 3. Staining methods - fluorescence

• use 2 dyes:
• 1. green fluorescening dye - penetrates all cells
• 2. red dye (Propidium iodide) - penetrates cells that dont have cell membranes (aka dead cells)

commercial name: BacLight

• -stain binds to DNA and strongly fluorescent when exposed to UV lights.
• -problem: stains both live and dead cells

• -good tracking a specific organisms within a habitat
• -specific antibody attaches to specific site
• -good for diagnosing infectious diseases and other lab work :-)

• -insert GFP into the geome and add to the natural population.
• -tags green (but not always green)
• -reporter gene - replace gene with GFP
• -problem: need oxygen

• -nucleic acid probe
• -obligonucleotide complementary to a sequence in a targe gene or RNA -hybridize)
• -hybridized to cells in a natural environment
• -doesnt kill microbe
• -can measure gene expression

PCR - polymerase chain rxn: artifical amplification of a DNA sequence by repeated cycles of strand separation & replication

DGGE - denaturing gradient gel eletrophoresis: separating nucelic acid fragments of the same size that differe in base sequence

ex - red fluorescent dye tag bacillus, green dye tag staph, etc.

• the total genetic complement of all cells present in a particular environment
• -detect as many as genes as possible that encode recognizable proteins & determine the phylogenetic groups to which it belongs to

• 1. Chemical Assays
• 2. Radioisotopes
• 3. Microelectrodes
• 4. Stable Isotopes

• direct chemical measurements of microbial rxn
• ex- fate of lactate oxidation by sulfate-reducing bacteria H₂S
• - not good for highly sensitivity

• - good for:
• 1. when high sensitivity is required
• 2. turnover rates need to be determined
• 3. fate of portions of a molecules needs to be followed.
• problem: some transofrmations might be due to abiotic prcesses

• -account the abiotic process in radioisotopes
• -yields proper control in experiment
• -ex formalin

• -small glass electrodes
• -measures: pH, Oxygen, N₂O, CO₂, H₂, or H₂S
• ex- shine the light, add electrodes = measures the amount of oxygen being generated

• -MAR
• -method that cells are exposed to a radioisotope and slided - photographic emulsion. darkness-decay =silver grains in the emulsuion

a method for characterizing an organism that incorporates a particular substrate by feeding the subsrate in ¹³C form and then isolating ¹³C-enriched DNA and analyzing the gene

• -one of two stable isotpe methods
• -discrimination by enzymes against the heavier isotope of various isotpes of C or S, leading to enrichment of the ligher isotopes.