Soils 412W Psu

Front 1

What are the three domains of life based on DNA sequencing?

Back 1

Bacteria, Archea and Eukarya

Front 2

Which of the three domains are prokaryotic?

Back 2

Bacteria and Archea

Front 3

What does prokaryotic mean?

Back 3

single celled and lacking a membrane bound nucleus

Front 4

What does eukaryotic mean?

Back 4

multicellular and unicellular organisms that have cells with a membrane bound nuclei and other organelles

Front 5

Which domain does soil microorganisms fall into?

Back 5

All three

Front 6

What are the older five Kingdoms?

Back 6

Monera, Fungi, Protists, Plants and animals

Front 7

Which kingdom do bacteria and arheaea belong to?

Back 7

former kingdom of monera

Front 8

What is phenotypic classification?

Back 8

How organisms act and behave. examples include what they eat, their size shape and mobility etc.

Front 9

What is phylogenetic classification

Back 9

based on evolutionary relationships and are determined from DNA sequencing.

Front 10

What are two distinct PHENOTYPIC groups of bacteria?

Back 10

Pseudomonas and Nitrosopira.
Pseu is aerobic, heterotrophic bacilli (rod shaped), nitrosospira is an ammonia oxidizing nitrifers, cocc or spiral shaped.

Front 11

What does bacilli mean?

Back 11

rod shaped

Front 12

what does cocci mean?

Back 12

Spherical

Front 13

Pseudomonas and Nitrosopira belong in what phylogenetic sudbdivion

Back 13

Beta proteobactera

Front 14

Pseudomonas (phenotypic)

Back 14

Heterotrophic, rod-shaped aerobes

Front 15

Clostridium (phenotypic)

Back 15

Heterotrophic, rod-shaped anaerobes

Front 16

Desulfovibrio (phenotypic)

Back 16

Heterotrophic, sulfate-reducing anaerobes

Front 17

Rhizobium (phenotypic)

Back 17

Heterotrophic, N2-fixing aerobes that form symbioses with legumes

Front 18

Azotobacter (phenotypic)

Back 18

Heterotrophic, N2-fixing aerobes that live freely in soil

Front 19

Actinomyces (phenotypic)

Back 19

Filament-forming, organic polymer degraders

Front 20

What was the first comprehensive reference that described the difference between bacteria and archaea?

Back 20

Bergey’s Manual of Systematic Bacteriology

Front 21

How do bacteria and archaea differ?

Back 21

in their cell walls and cell membranes. Also methane formation is a metabolic trait found only in archaea

Front 22

What does vibrios mean?

Back 22

comma-shaped

Front 23

what does spirilla mean?

Back 23

Spiral shaped

Front 24

what does actinobacteria mean?

Back 24

Thin branching filaments

Front 25

coccobacilli

Back 25

in between rod and cocci

Front 26

How big are cell diameters?

Back 26

.3-1 micron

Front 27

What is Step 1 of gram slide?

Back 27

Add crystal violet dye for 1 minute. dry gently

Front 28

What is step 2 of gram slide?

Back 28

Add iodine solution for 1 minute. wash off gently

Front 29

What is step 3 of gram slide

Back 29

add ethanol decolorizer for a few seconds. Wash gently

Front 30

What is step 4 of gram slide

Back 30

Add safranin "counter stain" for 30 seconds. wash off gently. Air Dry.

Front 31

What is step 5 of gram slide.

Back 31

Examine under microscope and look for pink or purple cells.

Front 32

What does a gram positive cell mean?

Back 32

Purple. Cell walls are simple (one layer of peptidoglycan) and crystal iodine and violet purple are tightly bound to the wall. They do not take up pink counter stain.

Front 33

What does a gram negative cell mean?

Back 33

Pink. More complex have an outer lipidpolysaccharide later over peptioglycan. the lipid layer releases crystal violet and iodine readily so counterstain is readily taken up

Front 34

What makes up a cytoplasmic membrane (cell membrane)

Back 34

is made up of a phospholipid and lies under the cell wall to from a semipermable barrier. Bacteria and archea have distinctly different phospholipid compositions to their cell membranes

Front 35

What are the three mechanisms by which nutrients enter the prokaryotic cell membrane?

Back 35

Diffusion, facilitated diffusion, and active transport

Front 36

What materials can pass through a cell membrane

Back 36

water, gases, small lipid-soluble molecules

Front 37

Which plates in a dilution are countable?

Back 37

plates with 20-200 colonies

Front 38

what is the correct way to report plate count results using standard microbiological format

Back 38

e.g., 1.3 x 108 cfu g-1 dry soil) use two sig figs followed by an exponent

Front 39

14. Be able to calculate numbers of cfu per gram of soil from the numbers of colonies on countable plates and the dilution factor

Back 39

YEAH LEARN THAT

Front 40

15. Know how to determine gravimetric moisture content of a soil sample.

Back 40

YEAH LEARN THAT TOO

Front 41

WEIGHT OF DRY SOIL = WEIGHT OF MOIST SOIL
__________

(1 + GRAVIMETRIC MOISTURE CONTENT)

Back 41

YEAH

Front 42

What do we know from DNA sequencing abut blue green algae?

Back 42

They are bacteria

Front 43

What does the term soil algae refer to?

Back 43

algae and cyanobacteria found on soils

Front 44

What are the three important functions of soil algae?

Back 44

CO2 fixation by oxygen photosynthesis, nitrogen fixation (some cyanobacteria only) and soil stabilization through mat formation and mucilage production

Front 45

What is the difference between cyano and algae about when they appeared on earth

Back 45

Cyanobacteria- 3.5 billion years ago, algae-1 billion years ago

Front 46

What is the difference between cyano and algae about their domain?

Back 46

cyano belongs to bacteria, algae is eukarya

Front 47

What is the difference between cyano and algae with respect to size?

Back 47

Cyano-.5-1 micron
algae 5-20 micron

Front 48

What is the difference between cyano and algae with sites of photosynthesis

Back 48

cyano-chlorphyll a phycobilns
algae-chlorophyll a, chlorophyll b or c

Front 49

What is the difference between cyano and algae in terms of fixing N2

Back 49

cyanbacteria: yes
algae: no

Front 50

What is the difference between cyano and algae in forming associations with lichens?

Back 50

cyan-yes
alg-no

Front 51

What is the difference between cyano and algae in terms of groups in soils

Back 51

cyan-unicellular, filamentous, filamentous with heterocysts
algae- unicellula, colonial, filamentous, branched filamentous, green, yellow green, brown diatoms

Front 52

What is the difference between fungal filament and bacteria filament?

Back 52

bacteria filament is composed of many individual prokarotic organisms whereas fungal filamentous consists of many cells of a single eukaryotic organis,

Front 53

what does extracellular mean and why is it important?

Back 53

it means that fungi release these enzymes into the environment. fungi use these in the decay process to degrade organic polymers into smaller molecules and possibly down to monomer units.

Front 54

Why are fungi excellent foragers of nutrients in soils?

Back 54

fungal hyphae are multicellula and have multiple mobile nuclei and vesicles which can move to other segments of hyphal filament that are located in nutrient rich soils.

Front 55

What do the vesicles in fungi do?

Back 55

Vesicles are fungal organelles rich in enzymes and energy compounds like lipids. vesicles can translocate along the hypha from a nutrient poor to a nutrient rich region of soil and provide a source of ATP and pre synthesized enzymes at the growing tips. this enable the fungues to form new tissue much more rapidly.

Front 56

are fungi auto trophs or heterotrophs

Back 56

heterotrophs

Front 57

What are fungal cell walls composed of?

Back 57

both plants and fungus have RIGID cell walls. fungal cell walls contain no cellulose, instead they contain chitin and non-cellulosic carbohydrate polymers.

Front 58

What is chitin?

Back 58

nitrogen containing carbohydrate polymer that is also found in insect exoskeletons.

Front 59

Why do some fungi appear black or dark colored?

Back 59

The cell walls of some fungi contain a protective, dark, pigment melanin which makes the cell walls more difficult to be degraded.

Front 60

What do you call fungal cell walls that have no pigment?

Back 60

Hyaline. decomposes faster

Front 61

What are the five phyla of true fungi

Back 61

Chytrids, Basidiomycota, Zygomycota, ascomycota, glomermycota

Front 62

Did true fungi have one common ancestor?

Back 62

yes

Front 63

How do we know that oomycota are not fungi?

Back 63

Because they did not descend form the same ancestor

Front 64

What is the difference between the fungal mycelium and fungal spores?

Back 64

The mycelium is a massive network of vegetative (non reproductive) hyphae. Mycelium may be septate (individual cells clearly separated by walls) or nonseptat (no obvious divisions. Mycelia grow by apical extension (growth from the tip). Fungal spores are non growing reproductive structures, usually spherical and pigmented. spores must germinate before a hypha can to begin to grow from it. Asexual spores germinate without the need for a union with another spore. Sexual spores germinate only after union with a spore from another mating type

Front 65

Which group of fungi have been implicated in diseases of frogs and other amphibians?

Back 65

Chytrids, which have motile life stage which enables them to swim in moist environments to infect new hosts

Front 66

Which fungi are the main "mushroom producers"

Back 66

Basidiomycetes. They bear their sexual spores on club shaped structures known as basidia. Many are also ECTOMYCORRHIZAL

Front 67

what does ECTOMYCORRHIZAL mean?

Back 67

mycorrhizal type in which the fungal mycelia enxtend inward, inbetween root and cortical cells, to form a network (hartig net) and outward into surrounding soil. Usually the fungal hyphae also form a mantle on the surface

Front 68

Which fungal group contains the most of the yeasts and plant pathogens?

Back 68

ascomyete. These fungi bear their sexual spores known as asci. some endomycorrhizal fugi belong to the asco

Front 69

endomycorrhizal

Back 69

mycorrhizal association with intra cellular penetration of the host root cortical cells by the fungus as well as outward extensions into the surrounding soil

Front 70

which group of fungi contains common food spoilage organisms called sugar fungi and bread molds?

Back 70

zygomycetes,

Front 71

What group do the common plant pathogens Pythium and Phytopthora belong to?

Back 71

These belong to oomycota. oomycota are protists

Front 72

mycelium

Back 72

mass of hyphae that form the vegetative body of many fungal organisms

Front 73

spore

Back 73

specialized reproductive cell. asexual spores germinate without uniting with other cells, whereas sexual spores of opposite mating types combine to from a zygote before germination occurs

Front 74

necrotrophic

Back 74

Nutritional mechanism by which an organism produces a battery of hydrolytic enzymes to kill and break down host cells and then absorb nutritional compounds from the dead organic matter

Front 75

biotrophic

Back 75

nutritional relationship between two organisms in which one or both must associate with the other to gain nutrients

Front 76

symbiotic

Back 76

living together in intimate association of two dissimilar organisms. the interactions can be commensal or mutualistic

Front 77

pathogenic

Back 77

ability of a parasite to inflict damage to the host

Front 78

obligate

Back 78

adjective referring to an environmental factor (for example, oxygen) that us always required for growth

Front 79

Facultative

Back 79

organism that can carry out both options of a mutually exclusive process

Front 80

chemotaxis

Back 80

oriented movement of a motile organism with reference to a chemical agent

Front 81

antagonism

Back 81

interaction between organisms where one organism is adversely affected and the other organism is unaffected

Front 82

mycophagous

Back 82

organism that consumes fungi, such as mycophagous nematodes

Front 83

rhizomorph

Back 83

mass of fungal hyphae organized into long thick strands usually with a darkly pigmented outer rind and containing special tissues for absorption and water transport

Front 84

sclerotium

Back 84

modified fungal hyphae that form a compact, hard, vegetative resting structure with a thick pigmented outer rind

Front 85

teleomorph

Back 85

sexual stage in reproduction in which cells are formed by the process of meiosis and genetic recombination

Front 86

anamorph

Back 86

asexual stage of fungal reproduction in which cells are formed by the process of mitosis

Front 87

holomorph

Back 87

whole fungus consisting of all sexual and asexual stages in its life cycle

Front 88

ergosterol

Back 88

a sterol, is a biological precursor (a provitamin) to vitamin D2. Sterols are an important class of organic molecules

Front 89

What do we mean when we say that the mycorrhizal symbiosis is a mutualistic relationship

Back 89

the plant produces carbon to the fungus, and the fungus acquires nutrients for the plant

Front 90

what percentage of all plant species form mycorrhizal associations?

Back 90

either 80% or 90%

Front 91

Which family does NOT form mycorrhizal associations

Back 91

the brassica plant family, because sulfur compounds in the plant tissue interfere with fungal colonization. these include brassica crops like broccoli, kale, collards, cabbage, cauliflower, brussel sporuts, rapeseed. growing brassica crops has been used as a way to "biofumigate" pathogens in soils with volatile sulfur compounds released by decaying plant tissue

Front 92

endo verses ecto

Back 92

endo: inside
ecto: outside

Front 93

What does AM fungus mean? What does VAm fungui mean

Back 93

These terms both refer to the endomycorrhizae and that AM fungi is now the preferred ter,. This is because all endomycorrhizae produce arbuscules but not necessarily vesicles

Front 94

arbuscle

Back 94

special tree shaped structure formed within root cortical cells by arbuscular mycorrhizal fungi

Front 95

ectomycorrhiza

Back 95

mycorrhical type in which he fungal mycelia extend inward, between root cortical cells to form a network (hartig net) and outward into surrounding soil. usually the fungal hyphae also form a mantle on the surface of the soil

Front 96

mycelia

Back 96

mass of hyphae that form the vegetative body of many fungal organisms

Front 97

endomycorrhiza

Back 97

nycorrhizal association with intracellular penetration of the host root cortical cells by the fungus as well as outward extension into the outer soil

Front 98

extraradical hypha

Back 98

are the hyphae that live outside of the roots of the host or partner plant.

Front 99

Hartig net

Back 99

is a hyphal network, that extends into the root, penetrating between epidermal and cortical cells. This network is a site of nutrient exchange between the fungus and the host plant.[1] Hartig net is typical for ectomycorrhiza.

Front 100

vesicle

Back 100

spherical structure, formed intracellularly, by some arbuscular mycorrhizae

Front 101

mantle

Back 101

The young roots usually branch and their ends thicken; the growing parts of the roots are enveloped by the thick, solid fungal sheath, from which emanate the fungal hyphae

Front 102

which plant hosts are all woody and mostly coniferous trees and some deciduous trees

Back 102

ectomycorrhizal plant hosts

Front 103

which plant hosts are mostly herbaceous (non-woody) plants but include many deciduous trees and a few coniferous trees

Back 103

endomycorrhizal plant hosts

Front 104

ericoid mycorrhizal hosts

Back 104

Ericaceous plants (heathers, azaleas, blueberries, cranberries, rhododendrons) and achlorophyllous Monotropa (Indian pipe). Ericoid mycorrhizae have forms intermediate between endo- and ectomycorrhizae.

Front 105

10. Is it possible for a plant to be “infected” by different mycorrhizal fungi?

Back 105

Yes, tree species that can support colonization on one plant by both ecto- and endomycorrhizae are alders (Alnus), willows (Salix), poplars (Populus), and eucalyptus trees.

Front 106

11. Describe how a nutrient depletion zone forms around a root. Is the size of the depletion zone the same for different nutrients, like N and P?

Back 106

Be sure to know which nutrients are diffusion-limited in the soil solution. Phosphorus is diffusion-limited (low mobility) because phosphate has low solubility at neutral pH. When P is depleted, therefore, it is replenished by diffusion only extremely slowly through the soil solution. See Fig. 12-7 for differences between N and P. With respect to N forms, nitrate is more mobile than ammonium. Although both forms of N are soluble, ammonium is retained by negatively charged sites on soil colloids, while nitrate is NOT diffusion-limited.

Front 107

12. What are the main mechanisms by which mycorrhizal fungi benefit plant growth?

Back 107

a. Fungal hyphae are more narrow than plant roots so they can enter soil pores inaccessible to roots; b. hyphae also increase total absorbing surface areas of roots, especially surface areas outside nutrient depletion zones; c. fungi excrete oxalic acid, which helps dissolve inorganic phosphates by lowering pH; d. fungi produce phosphatase enzymes that break bonds between phosphate and organic carbon groups.

Front 108

13. How much of the total carbon (photosynthate) produced by plants becomes transferred to the mycorrhizal fungus?

Back 108

See estimate on page 273, or 20%.

Front 109

14. Under which TWO conditions might mycorrhizal infection be a “drain” on the plant?

Back 109

see page 273

Front 110

15. What is glomalin? What effect does glomalin have on soil properties?

Back 110

?

Front 111

16. What are four mechanisms by which mycorrhizal fungi protect plants from root pathogens

Back 111

a. create a mechanical barrier; b. produce antibiotics; c. compete for nutrients; and d. induce generalized defense mechanisms in the plant host.

Front 112

17. Which types of plants benefit more from mycorrhizal infection?

Back 112

Coarse-rooted plants (like legumes) benefit more than fine-rooted plants.

Front 113

18. What are two ways by which the mycorrhizal symbiosis benefits the ECOSYSTEM?

Back 113

a. can offset drought conditions by making plants more drought-tolerant; b. can improve soil structure by increasing organic matter content in soils.

Front 114

19. What are factors that can REDUCE mycorrhizal colonization of plants?

Back 114

a. conventional tillage; b. high applications of phosphate fertilizers; c. planting of cruciferous crops; d. leaving soil fallow (no plants); e. use of pesticides, particularly fumigants.

Front 115

EXTRA CREDIT QUESTIONS:

Back 115

Approximately how many meters of endomycorrhizal fungal hyphae can be found in a single gram of soil?
What is the difference between infective and effective inoculants?