week 1: Introduction to microbial diversity and soil microbiome

Question 1

prokaryotes vs eukaryotes vs archaea

Answer 1

prokaryotes: organisms that lack a nucleus that protects the DNA/genome (bacteria and eukarya)

eukaryotes: organisms that have a nucleus

archaea: extremophiles, cell walls are different in composition than others such as a bacterial cell

Question 2

traditional ways to differentiate bacteria

Answer 2

1. shape of cells/cell structure
2. gram staining
3. aerobic/anaerobic/facultative anaerobe
4. physiology: nutrient requirements, metabolism

Question 3

Describe gram-positive and gram-negative structures

Answer 3

gram positive: thick layer of peptidoglycan

gram negative:
-thin layer of peptidoglycan
-outer membrane made of LPS and protein
-periplasm between outer membrane and cytoplasmic membrane

peptidoglycan gives cell wall rigidity

Question 4

gram stain procedure

Answer 4

1. add methanol to fix cells to surface
2. add crystal violet stain
3. add iodine (binds stain to gram-positive cells)
4. wash with ethanol
5. add safranin counterstain

gram positive: purple
gram negative: pink

Question 5

16S rRNA in ribosome

Answer 5

-binds to the shine-delgarno complementary sequence in prokaryotic mRNA

Question 6

16S rRNA gene (what is it used form advantages and disadvantages to bacteria identification by using this)

Answer 6

-used for bacterial identification
-encodes the 16S rRNA that forms part of the ribosome (the 30S subunit)
-contains 9 variable regions used to classify and identify bacteria

advantages:

-do not need to culture/grow the bacteria
-can amplify the gene encoding 16S rRNA sequence by PCR then sequence the gene as long as the bacterial DNA is present in the sample
-less time-consuming

disadvantages:

-dependent on matching to already identifies bacteria from the database
-may lack resolution to distinguish between different strains
-cannot reveal metabolic capabilities or functional diversity
-high risk of contamination

Question 7

diversity of the soil microbiome

Answer 7

-oxygen concentration gradient
-fungi and heterotrophic bacteria (actinomycetes and proteobacteria) catabolize organic material

synergy and nutrients, competition affect the types of microorganisms in the soil