Week 13 Diversity Of Marine Microbes

Question 1

Why is SSU ribosomal RNA an ideal chronometer?

Answer 1

1. Present in all organisms
2. Slow mutation rate
3. Performs an identical function in all organisms

Question 2

What can be used to compare the phylogeny of close and distinct taxa?

Answer 2

Nucleotide or inferred amino acid sequence

Question 3

What is ARB-Silva?

Answer 3

The biggest database of SSU and LSU rRNA

Question 4

How were bacterial/archaeal species operationally defined in teh past?

Answer 4

1. Distinctive phenotype property

2. Genomically coherent - DNA-DNA HYBRIDISATION >70%

Question 5

Using 16S rRNA gene sequencing, what is the definition of a species?

Answer 5

> 97%

Question 6

Using whole genome sequencing what is the definition of a species?

Answer 6

95-96% average nucleotide identity

Question 7

What is a candidates species>

Answer 7

Uncultured bacteria that cannot be assigned to a valid species because we do not have the full information about their phenotype

Question 8

What is an operational taxonomic unit

Answer 8

Sequences grouped on the basis of similarity - without saying for sure if its a species

Question 9

What are amplicon sequence variants?

Answer 9

Sequences that aren’t grouped

Question 10

What happens when you use whole genome sequencing instead of 16S rRNA sequencing to define a species?

Answer 10

Some of the positions of microbes have been further shifted

Question 11

What does this image show? (2 things)

Answer 11

1. Bacteria is highly diverse

2. There are significant differences between pelagic and benthic microbes

Question 12

What are the most numerically abundant bacteria?

Answer 12

Proteobacteria

Question 13

Name at least three common marine bacteria?

Answer 13

1. Cyanobacteria
2. Bacteroidetes
3. Actinobacteria
4. Chloroflexi

Question 14

What are a-proteobacteria?

Answer 14

Metabolic generalists

Question 15

What is the most common bacterial species in the ocean?

Answer 15

A-proteobacteria - SARS 11

Question 16

What are b-proteobacteria a part of?

Answer 16

Y-proteobacteria

Question 17

What 3 main functions do y-proteobacteria have?

Answer 17

1. POC mineralises
2. Oxidation of ammonia
3. Oxidation of methane
4. Oxidation of sulphide

Question 18

What are planctomycetes associated with?

Answer 18

Marine snow and an anammox bacteria

Question 19

Many bacteroidetes and planctocytes harbour taxa that have what function?

Answer 19

Degradation of complex organic compounds

Question 20

Marine archaea were long believed to be thermophiles, what have they also been discovered to be?

Answer 20

Living mesophillic lifestyles

Question 21

How much abundance does marine archaea have in the twilight zone?

Answer 21

Up to 40%

Question 22

What can Marine Group 1 do that was thought to only be in proteobacteria?

Answer 22

Ammonia oxidising

Question 23

What important function does crenarchaeota have?

Answer 23

Chemolithoautotrophic through sulphur reduction

Question 24

What other roles do archaea have in recycling?

Answer 24

Roles in methane and nitrogen cycling

Question 25

What does this image show?

Answer 25

That archaea classification is rapidly changing and is key for the emergence of eukaryotes

Question 26

What is DPANN

Answer 26

Archaea closely related to LUCA with bacteria

Question 27

What is a prevalent role for protists and marine fungi?

Answer 27

Important degrades of organic matter

Question 28

How do protists reproduce?

Answer 28

Sexual recombination

Question 29

Protists are highly divers, how much do we know?

Answer 29

Not a lot

Question 30

What are two major roles of marine fungi?

Answer 30

1. Degrade complex hydrocarbons (oil)

2. Colonisation and degradation of plastic debris

Question 31

How do marine fungi feed?

Answer 31

Heterotrophic osmotrophs

Question 32

What are two features of viruses?

Answer 32

1. Can be DNA o RNA

2. Their size can be variable

Question 33

How can viruses impact communities?

Answer 33

Affect the structure and diversity of microbial communities and manipulate life histories through co-evolution

Question 34

Name four types of ways that protists can feed?

Answer 34

1. Predators
2. Osmotrophs
3. Saprotrophs
4. Mixotrophs