Micro 3

Front 1

photoautotrophs

Back 1

get energy from sunlight through photosynthesis

Front 2

chemolithotrophs

Back 2

use inorganic chemicals to get energy (ATP)

-hydrogen oxidation

sulfur oxidation

iron oxidation

nitrification

Front 3

chemoorganotrophs

Back 3

use organic chemicals to gain energy

Front 4

heterotrophs

Back 4

get their carbon from an already existing organic source

Front 5

photoheterotrophs

Back 5

get energy from sunlight, but C from organics

Front 6

light dependent reactions

Back 6

uses sunlight to generate ATP and NADPH

Front 7

light independent reactions

Back 7

uses ATP and NADPH to fix CO2 into organic forms

Front 8

oxygenic photosynthesis

Back 8

produces O2 as a byproduct. breaks down water

Front 9

anoxygenic photosynthesis

Back 9

does not produce oxygen as a product. can break down H2S

Front 10

sunlight is captured by

Back 10

pigment molecules-

chlorophyll in plants and some bacteria

bacteriochlorophyll in others

Front 11

photosystems

Back 11

-what pigments are arranged into.

-they are embedded in a membrane.

-cholorplasts with thylakoids in plants.

-usually in a derivative of cell membrane in prokaryotes

Front 12

accessory pigments

Back 12

-collects light energy and pass it along to the reaction center.

-absorb at other wavelengths than chlorophylls.

-absorb wavelengths and pass energy to chlorophylls.

Front 13

reaction center

Back 13

specialized chlorophyll molecule that will use the sunlight energy to generate ATP

Front 14

Anoxygenic photosynthesis

Back 14

aka cyclic photophosphorylation

-uses sunlight to generate ATP

-oxidizes an inorganic molecule to generate NADPH

.. as sunlight excited accessory pigments, the energy is passed along to the reaction center where an excited e- moves to a higher energy shell. it is passed to an ETC and a proton gradient is set up to make ATP. e- returns to starting point

Front 15

oxygenic photosynthesis

Back 15

aka noncyclic photophophorylation

-electrons don't go back to the starting point

-e-s pass thru an ETS to reduce NADP to NADPH

-.. have to replace e- from another source

Front 16

light independent reactions (dark Reactions)

Back 16

after ATP and NADPH are generated they are used to make organic C

- does not require sunlight directly, hence the "dark" reactions

-does require products of the "light" reactions

Front 17

the calvin cycle

Back 17

fixes inroganic CO2 into organic C (glucose)

CO2 combines with RuBP (5C molecule)

6c is unstable and breaks in 3C (PGA)

PGA is phosphorylated (break down ATP) and rearranged (uses NADPH) into G3P

G3P can be converted to glucose

have to regenerate RuBP

use 6 Co2 at a time (6 C for glucose)

Front 18

anaerobic respiration

Back 18

uses something other than O2 as the terminal e- acceptor. such as

-iron

-nitrate

-fumarate

-sulfate

(varying levels of ATP produced)

-carbonate

Front 19

nitrate and sulfate

Back 19

commonly reduced e- acceptors

can be assimilative or dissimilative

Front 20

assimilate

Back 20

becomes a part of a process. can be used as a nutrient

Front 21

dissimilate

Back 21

is released from the process. is useless to everyone

Front 22

nitrate reduction and denitrification:

Back 22

nitrate = terminal e- acceptor

reduced thru several steps

many products are gaseous -->

released (dissimilated) into atmosphere=

(denitrification)

Front 23

sulfate reduction

Back 23

assimilative or dissimilative

ass: SO4 converted into organic form of sulfur (amino acids)

diss: produces H2S

Front 24

methanogensis

Back 24

anaerobic resp

reduced CO2 to CH4

various coenzymes used

Front 25

fermentation

Back 25

glucose and other molecules can be fermented leading to various products and amounts of energy

Front 26

nitrogen fixation

Back 26

converts N2 gas into ammonium ions (NH4+)

ammonium can then be incorporated into amino acids (organic n)

requires enzyme: nitrogenase

Front 27

nitrogenase

Back 27

-enzyme used in nitrogen fixation

-only functions under anaerobic conditions

-live in areas where O2 levels are controlled

-many are symbionts with plant roots

...plant provides food, shelter, bound O2

....... O2 bound to hemoglobin in plant available to bacteria in roots

bacteria in roots provide fertilizer for plant

Front 28

guilds

Back 28

a microbe population that is metabolically related

Front 29

community of microbes

Back 29

a set of guilds of microbes

Front 30

microbes interact with

Back 30

other species of microbes

macrobes

Front 31

microbial ecology

Back 31

how microbes interact with each other and their environment.

Front 32

objectives of Microbial Ecology

Back 32

1. understand biodiversity and their interactions

2. measure activities of microbes and monitor effects on ecosystems

Front 33

microbes require

Back 33

the proper nutrients and conditions

Front 34

niche of a microbe

Back 34

the differences in the required nutrients and conditions of microbes

Front 35

microenvironment

Back 35

where microbes live

various microenvironments -->many diff microbes in close proximity

(anaerobes, aerobes, microaerophiles)

Front 36

biofilm

Back 36

occurs when many microbes attach to a surface. they are encased in films of polysaccharides which helps to trap nutrients and attach them to the surface

i.e. dental plaque

Front 37

feast or famine

Back 37

nutrients may be scarce or plentiful depending on the time.

because of this, microbes are rarely in exponential growth.

-generation times are much slower

Front 38

scarce nutrients...

original theory of antibiotics

Back 38

microbes compete for nutrients

antibiotics were a way to kill off the competition

Front 39

syntrophy

Back 39

microbes interact instead of compete- one produces something that is needed by the other

Front 40

enrichment culture methods

Back 40

used to grow microbes from the environment

-use medium and conditions to select for desired microbe

-frequently have to go thru successive steps

i.e. Winogradsky

Front 41

after enrichment

Back 41

microbe must be isolated,

if it grows on plates, streak one. or do an agar shake

Front 42

agar shake

Back 42

suspends cells in agar- they grow as isolated colonies embedded in the agar

Front 43

genetic analysis

Back 43

used to determine which organisms are present without growing them

-isolate DNA or RNA from a community

sequence or use probes to determine what organisms are present

Front 44

terrestrial environments

Back 44

-microbes in soil mineral and organic soils

-plants also grow in soil and secrete materials --rhizosphere

-soil consists of many different chemicals and microenvironments

Front 45

O horizon

Back 45

layer of undecomposed plant materials

Front 46

A horizon

Back 46

surface soil (high in organic matter, dark in color, is tilled for agriculture; plants and large numbers of microorganisms grow here; microbial activity high)

Front 47

B horizon

Back 47

subsoil (minerals, humus, and so on, leached from soil surface accumulate here; little organic matter; microbial activity detectable but lower than at A horizon)

Front 48

C horizon

Back 48

soil base (develops directly from underlying bedrock; microbial activity generally very low)

Front 49

single particle of soil

Back 49

may contain organic material as well as inorganic

may or may not contain water and oxygen

may have a number of microenvironments in one particle-- many microbes

Front 50

most microbes grow

Back 50

in the surface areas of soils

-higher levels of oxygen and usually organics

Front 51

some microbes grow

Back 51

in deep subsurface environments

-typically very slow growers, but may be important in bioremediation

Front 52

aquatic environments

Back 52

includes freshwater and marine

Front 53

most photosynthesis in aquatic habitats is done by

Back 53

bacteria

Front 54

marine environments are

Back 54

pretty homogenous when compared to freshwater

conditions don't change much

Front 55

freshwater habitats have

Back 55

a variety --> variety of nutrients and conditions.

stratification- based on oxygen ad light penetration

aerobic near top, anaerobic at the bottom

perhaps a big Temperature difference

Front 56

level of organic material in freshwater

Back 56

may fluctuate

especially rivers where wastewater is returned after treatment

if lots of organics are added, expect more growth of microbes and macroorganisms

water has a high BOD

Front 57

hydrothermal vents

Back 57

specialized deep sea environment.

-animal communities supported by growth of bacteria

-very hot sea water vents from these areas, mixed with minerals.

typically lots of sulfur or ammonium.-->support growth of chemilithotrophs

---provide food for animals living in association with the vent

bacteria may grow in symbiosis with the animals (in gills)

Front 58

biogeochemical cycles

Back 58

microbes used in recycling many elements

-include both organic and inorganic forms of various elements

Front 59

carbon cycles

Back 59

through that atmosphere, land, and water

Front 60

humus

Back 60

dead organic material that is broken down by microbes (bacteria & fungi)

converts humus into Co2 thats returned to the atmosphere

Front 61

coupled cycles

Back 61

carbon and nitrogen.

changes in one cycle can affect the other

Front 62

nitrogen cycle

Back 62

involved organic and inorganic forms

atmospheric N2 can be converted into NH3 by nitrogen fixation (organic)

NH3 can be used or broken down through nitrification/denitrification

assimilative/dissimilative processes

Front 63

sulfur cycle

Back 63

SO4 is the organic form

can be produced from elemental sulfur or from H2S

ass/dissim

Front 64

iron and manganese cycles

Back 64

microbes can cycle ironbetween the ferric (3+) and ferrous (2+) forms

means they can leach iron out of pipes

also frequently leach iron out of pyrite (byproduct of coal mining)--> acid mine drainage

Front 65

manganese exists in

Back 65

mainly 2 oxidation states.

can also be oxidized and reduced

Front 66

microbes can also be used to

Back 66

leach other minerals (especially copper)

ores that contain a little copper are acidified

bacteria will extract the copper under the acidic conditions provided

Front 67

microbes can be used to bioleach gold and uranium

Back 67

uranium leaching depends on the oxidation of U4+ to U6+ by Fe 3+ with A. ferrooxidans reoxidizing Fe2+ to Fe3+

gold is deposited with minerals containing arsenic and FeS2

A ferro can leach the arsenic and pyrite. gold is then complexed with cyanide

Front 68

mercurytrasnformation

Back 68

elemental mercury is a byproduct of plastics manufacture

when dumped in water it settles into the sediment

anaerobes convert it into methylmercury, which is highly toxic

Front 69

bioremediation

Back 69

can sometimes use microbes to clean up our messes

uranium contamination of groundwater occurs where uranium has been processed or stored

Front 70

some bacteria can convert

Back 70

U6 to U4

U6 is water soluble

U4 is not

uranium is contained not removed

Front 71

bioremediation of oil spills

Back 71

naturally occurring bacteria bacteria can degrade hydrocarbons

deepwater horizon oil leak in 2010

not as bad as it could have been due to natural microbe action

Front 72

Exxon Valdez tanker spills in 1989

Back 72

about 10m gallons of crude oil spilled in Prince William Sound, AK

contaminated 1300 miles of remote coastline

sprayed coast with microbes and fertilizer

Front 73

bioremediation of xenobiotics

Back 73

chemically synthesized compounds that don't occur naturally

-pesticides

-PCBs

may serve as a nutrient or a co-metabolite

(broken down while another molecule is used as a nutrient)

Front 74

Wastewater treatment

Back 74

treat water to remove wastes, including sewage.

industrial wastes are a different problem.

typical, municipal wastewater treatment is concerned with levels of sewage

Front 75

goal of wastewater treatment

Back 75

to reduce levels of organics in water

measured through BOD

Front 76

BOD

Back 76

biological oxygen demand

more organics means microbes would require more oxygen to break them down

can measure amount of O2 used to break down material in water

Front 77

primary treatment

Back 77

screening &sedimentation

physical process

large particle filtration followed by settling.

usually does not remove most of the organic material in water so continue on to next step

Front 78

secondary treatment

Back 78

activated sludge/aeration

trickling filter (aerobic)

biological processes. use microbes to remove organics in water. can be either aerobic process or anaerobic

Front 79

anaerobic digestion -->

Back 79

digested sludge: drying, incineration; use as fertilizer, or burial

Front 80

aerobic oxidation--->

Back 80

disinfection --> treated effluent to discharge

Front 81

anoxic secondary treatment produces

Back 81

gases (including methane) as a byproduct

undigestible material left over -landfill

Front 82

aerobic treatment may use 2 processes:

Back 82

trickling filter bed- rocks colonized by microbes

.. water is dripped over the rocks and trickles down through filter bed

organics are removed

activated sludge

Front 83

wastewater pumped into large vat

Back 83

heavily aerated

bacteria etc grow in the water

when organics are removed, cells settle out

used in next process (i.e. activated sludge)

Front 84

sludge may be further treated

Back 84

anaerobic digester or composted

if BOD is still now low enough, further treatment may be necessary

tertiary

Front 85

Tertiary treatment

Back 85

chemical treatment

-activated charcoal

-reverse osmosis

Front 86

enhanced biological phosphorous removal

Back 86

uses phosphorous accumulating organisms

sequential passage through anaerobic and aerobic bioreactors

Front 87

concerns for wastewater treatment

Back 87

new biologically active contaminants that we have to remove from water

-pharmaceuticals

-sunscreen

-household products

-personal care products

Front 88

drinking water treatment

Back 88

waste water through secondary treatment is not yet drinkable.

need to continue to treat to remove pathogens, tastes and odors, chemicals and decrease turbidity

Front 89

drinking water purification involves a three step process

Back 89

sedimentation

coagulation and filtration

disinfection

sedimentation allows settling of large particles (sand, etc)

Front 90

coagulation involves

Back 90

coagulation involves addition of alum

causes "flocs" to form (bacteria and smaller particles aggregated)

flocs settle out

water is filtered through a sand bed

disinfection to remove any further pathogens

Front 91

disinfection usually means

Back 91

chlorination

high enough levels so that residual chlorine present as water moves through pipes

Front 92

water must be delivered

Back 92

travels through municipal and domestic pipes to reach destination

problems may develop:

-taste or odor

-growth of pathogens

select for resistant pathogens

Front 93

industrial microbiology

Back 93

uses microbes to produce commercial products

i.e: foods, pharmaceuticals and chemicals

microbes used for biocatalysis

use "fermentation" for everything

Front 94

industrial microbes must be

Back 94

stable in culture

grow rapidly

produce product in shor time

produce high yields

grow on inexpensive medium

be able to genetically manipulate

Front 95

products from cells are either primary or secondary metabolites

Back 95

primary- necessary for cell growth

produced in log phase.

i.e. AA's or alcohol

secondary- not necessary for growth

produced in stationary phase

i.e. antibiotics

Front 96

industrial processes take place inside a

Back 96

fermenter

a big vat 500,000 liters

most processes are aerobic, so sterile air must be introduced

system requires stirring to mix air into medium

characteristics:

adjust ph, heat/cool

drain tank, sample valve

Front 97

have to scale up to fermenter

Back 97

start small- test tube, move up. 50 ml, 500ml, 5 L. check conditions along the way

Front 98

antibiotic fermentation

Back 98

produced by microbes to kill other microbes.

secondary metabolites

frequently produced by fungi or actinomycetes

screening to find new antibiotics.

Front 99

once have antibiotic producer

Back 99

determine growth conditionsdetermine scale up procedurealso need to figure out how to recover antibioticfrequently released into medium so just have to separate it.

can also try to increase yield of antibiotic

-induce mutations

amplify genes for more copies

alter regulatory systems to produce increased yield

Front 100

antibiotic producer example: penicillin

Back 100

produced by mold- penicillium

secondary metabolite, so want to get to the stationary phase fairly quickly

Inoculate P. chrysogenuminto wheat bran- nutrient solutionGrow with forced aeration

Transfer into production tank(200,000 L) and grow on “corn steep liquor”

Continue aeration, grow for about7 daysPen G secreted into mediumSeparate cells from medium, drycells and sell as animal feed supplementAdd potassium to crystallize PenG

“Natural” penicillin is noteffective now

So Pen G is modified in thelaboratoryCalled semisyntheticpenicillinsModify the molecule so b-lactamasescannot inactivate the antibiotic

Front 101

other pharmaceuticals

Back 101

vitamins

AA's

both used as diet supplements for humans and animals

Front 102

bioconversions

Back 102

catalyze chemical conversions that are not easy to do in lab

major use in manufacturing steriods

Front 103

enzymes

-proteases

-amylases

-invertase

Back 103

- use in detergents and meat tenderizers

-making bread, detergents

-soft centered candies

Front 104

some enzymes are immobilized

Back 104

allows them to participate in biocatalysis without the organism

bind to carrier

polymerize molecules together

include enzyme in fibers or microcapsules

Front 105

Production of Wine:

Back 105

Wild yeasts are found on grapes -most fermentations don’t use theseCrush grapes to release juice(must) redwine is red grapes whiteis white grapes or skinless redAdd sulfur dioxide to kill yeasts

add winery yeasts

Allow fermentation in cask (oak,cement, stainless steel, etc.)Rack the wineAge the wineBottle and further age or sell

Front 106

vinegar

Back 106

Produced from alcohol which isconverted to acetic acid3 major methods - open-vat tricklemethod bubblemethod

Front 107

yeasts

Back 107

-Can be both product and producer

-Yeasts are sold as feedsupplements

-Products include bread andalcoholic beverages, vitamins

-Production of yeasts is anaerobic process, alcohol is anaerobic

Front 108

production of cheese

Back 108

-Curdle milk using rennin (enzyme)or a culture of Streptococcuslactis

-Separate curds (solids) and whey(liquid)

- Use solids for most cheeses

- Compress curds and squeeze outexcess water

-Allow curds to dry and compress

-Add various microbes to “ripen”the cheese: Propionibacterium for Swiss cheese (CO2 makes holes)

Molds (Penicillium) for bleu and Camembert cheeses

Front 109

symbioses

Back 109

relationships between organisms

mutualism

commensalism

parasitism

Front 110

mutualism

commensalism

parasitism

Back 110

beneficial to both

beneficial to one but doesn't affect the other

benefit to one party but harms the other

Front 111

microbe-microbe interactions

Back 111

lichens are fungus and photosynthesizer (algae or cyanobacteria)

often found growing on rocks, trees

-Photosynthesizerprovides organic molecules while fungus provides protection from erosion andsome minerals

Front 112

Plant-Microbe Interaction:

Back 112

Nitrogen fixation is symbiosis betweenleguminous plant and nitrogen-fixing bacteria. Bacteria produce nodules on plantroot and live inside

Provide “fertilizer” for theplant

Front 113

plant microbe interaction step 1:

recognition

Back 113

plant secretes AAs into rhizosphere--attracts Rhizobium

rhizobium recognizes and attaches to lectins on root hairs

Front 114

plant microbe interaction step 2: invasion

Back 114

Bacteria secrete chemicals thatcause root hair to curlaround the bacteria

Bacteria digest a hole into roothair and enter cell

Digest an infection thread back toward the main root

Front 115

plant microbe interaction step 3: travel

Back 115

bacteria move thru infection thread to main root

Front 116

plant microbe interaction step 4: formation of bacteroids

Back 116

pleomorphic cells, capable of nitrogen fixation

Front 117

plant microbe interaction step 5: tumor formation

Back 117

bacteria stimulate root cells to divide, forming the nodule

bacteria replicate inside nodule and fix nitrogen

plant gets a source of fertilizer, bacteria get a place to live and nutrients

Front 118

nitrogen fixing enzymes are sensitive to oxygen

Back 118

need some for cell growth

leghemoglobin in plant binds to oxygen and provides a source for bacterial cell growth

because oxygen is bound it does not activate the enzyme system

Front 119

agrobacterium

Back 119

causes crown galls (tumors)

Contains a plasmid, which can beused to shuttle DNA into plant cellsCloning vector for plantsInsert desired DNA (diseaseresistance) into plasmid, infect plant

Front 120

mycorrhize

Back 120

interactions between a fungus and a plant root

Front 121

ectomycorrhizae

endomycorrhizae

Back 121

fungi that grow around the plant root, but don't penetrate

penetrate into the root cells

Front 122

animal and microbe interactions

Back 122

Termites and gut symbionts

Microbes in termite gut are ableto digest cellulose that termites can’t

Front 123

ruminants cannot digest cellulose

Back 123

collection of microbes in ruminant stomachs help

fermentation in either foregut or hindgut depending on animals

Front 124

animals cannot digest cellulose

Back 124

collection of microbes in part of digestive tract help

fermentation in either foregut (ruminants) or hindgut (primates) depending on animal

Front 125

rumen

Back 125

special organ for fermentation that ruminants have

cows implanted with sampling ports

contains 10^10 to 10^11 microbes per gram of contents, mostly anaerobes

also synthesize AA's and vitamins for host

Front 126

microbes in human gut affect

Back 126

early development, health and predisposition to disease and maybe behavior

linked to obesity

provide some AA's, enzymes and vitamins