Lecture 17: Marine Microbes and their Significance in Biogeochemical Cycles

Question 1

What is Sulfur?

Answer 1

1. Atomic no. 16
2. ~1% of dry weight of organisms
3. Two mineral forms:
   a. Sulfide (S^2-)
   b. Sulfate (S04^2-)
4. Used as:
   a. fertiliser (plants = high demand)
   b. Manufacturing insecticides, fungicides,
   etc.

Question 2

Why is sulfur important?

Answer 2

1. Metabolism - fuel and respiratory
   electron donor
2. Proteins - AAs; cysteine and methionine
3. Disulphide bonds - protein stability +
   structure
4. Cofactors in enzymes - e.g., FeS in
   Aconitase (TCA cycle)
5. Antioxidant molecules glutathione and
   thioredoxin

Question 3

What are the different sulfur processes in microbes?

Answer 3

1. Assimilation - using sulfate to form 
   organic compounds (E dependent) 
   (animals use preformed S-compounds)
2. Dissimilatory sulfur metabolism - bacteria 
    and archaea use sulfur in E yielding 
    reactions (Ox or An)
3. Electron acceptors or donors (e.g., 
    Sulfate reduction & oxidation)
4. Generating signalling molecules
5. Generating anti-stress molecules

Question 4

What does assimilate mean?

Answer 4

Get something into a form that is useable

Question 5

Explain assimilatory uptake of sulfate

Answer 5

1. Sulfate abundant in marine environments
   (~10^6 x more abundant than other S)
2. Some incorporated into polysaccharides
3. Sulfate reduced to Sulfide in many
   microbes (requires E)
4. Sulfide used to make AAs cysteine and
   methionine

Question 6

What are different types of organisms transforming sulfur

Answer 6

1. Phytoplankton
2. Seaweeds
3. Few species from angiosperms
4. Some corals
5. Many heterotrophic bacteria

Question 7

What is marine DMSP synthesis?

Answer 7

1. Reduce sulfate to Sulfide to make 
   methionine (all req. E)
2. L-methionine is then turned into 
    "Dimethylsulfoniopropionate" (DMSP)
   a. stable and soluble zwitterion ( can be + 
       & - charged
   b. Prod. at v high [mM] e.g., 1/2M
   c. > 8 billion tonnes made per year
3. E.g., 
   a. Some marine eukaryotes
   b. Marine bacteria (Alphaproteobac teria)

Question 8

Why is DMSP produced?

Answer 8

1. Suggested roles:
   a. Osmoprotectant - OSMOLITES
   (balancing the osmotic difference
   between cell’s surroundings and
   cytosol)
   b. Cryoprotectant - CRYOLITES
   (maintaining enzyme activities in
   high and low temperatures)
   c. Grazing deterrent - deters predators
   due to their bad taste/toxicity
   d. Oxidative stress protectant -
   ANTIOXIDANTs DMSP and its
   catabolites scavenge oxygen free
   radicals generated by oxidative
   stress
   e. Storage molecule for carbon and
   sulfur - lots of carbon and sulfur in
   its structure so can be broken down
   at a later date

Question 9

Why only suggested roles?

Answer 9

none have been definitively established

Question 10

Why is it that we do not know the single gene or enzyme involved in these DMSP pathways, yet we know the biochemical synthesis pathways?

Answer 10

1. Marine biology generally lacking in 
   molecular biological approaches 
   compared to terrestrial systems
2. Marine eukaryotes that make DMSP lack 
     genetic manipulation tools

Question 11

What is known about DMSP pathways?

Answer 11

1. > 8 billion tonnes is made annually in
   surface oceans
2. 3-10% of global marine primary carbon
   production (GPP)
3. DMSP catabolism supplies 3-10% of
   carbon requirements of heterotrophic
   bacteria
4. DMSP supplies 50-100% of sulfur
   demands for heterotrophic bacteria
   (despite there being 1-10 million x more
   sulfate) VIA CATABOLISM

Question 12

What is DMSP catabolism

Answer 12

1. organisms eat DMSP and gain benefits 
   such as E, carbon, sulfur
2. DMSP - major nutrient for heterotrophic bacteria (N & S) (& E)
   a. 3-10%  of carbon supply
   b. 30-100% sulfur supply

Question 13

What are the two pathways for DMSP catabolism

Answer 13

1. Sulfur - demethylation pathway
   a. dmd genes
   b. 70% of DMSP in marine environment
   eaten forms MeSH (methanethiol)
   c. MeSH used as a source of sulfate

Question 14

What is SAR11 bacteria?

Answer 14

1. most abundant and ubiquitous clade of
   heterotrophic marine bacteria (1/3 of
   cells in photic zone)
2. Examples
   a. Candidatus Pelagibacter ubique - 1st
   cultured
   b. P. ubique genomes small (1.3Mbp)
   c. smallest no. genes in a living organism
   d. pathways for all 20 AAs and most
   cofactors
3. these bacteria have lost the genes allowing assimilation of sulfate into Sulfide
   a. therefore need reduced sulfur sources

Question 15

What is DMSP lysis?

Answer 15

1. ddd genes
2. approx. 30% of DMSP eaten generates
   Dimethylsulfide (DMS)

DMSP -> DMS + Acrylate or 3-hydroxypropionate

Question 16

What can SAR11 do?

Answer 16

DMSP to produce MeSH (using dmd genes) for sulfur, or produce DMS (using dddK genes)for carbon

Question 17

What are other examples of bacteria heterotrophic bacteria that lyse DMSP?

Answer 17

1. (alpha) Roseobacter

2. (gamma) Halomonas

Question 18

What are Roseobacters?

Answer 18

1. marine alpha-proteobacteria
2. 10-25% bacteria in marine surface
   waters, sediments and sea ice
   (abundant)
3. Easily cultured (ADVANTAGE OVER
   SAR11 FOR STUDIES)
4. Many genomes available
5. Just as abundant SAR11 but more diverse
   (more genera)

Question 19

What is the problem with SAR11?

Answer 19

1. VERY DIFFICULT TO CULTURE
   a. cant grow on plates
   b. cant isolate single colonies
   c. can only grow in liquid culture
   d. difficult to monitor growth and its rate

Question 20

Why is roseobacter a good model organism?

Answer 20

1. First studied: Ruegeria pomeroyi DSS-3
2. Isolated from DMSP enrichments of coastal Georgia Seawater
3. Genome sequenced in 2004
4. Genetically tractable
5. Much like SAR11:
   a. can produce DMS (using dddP, dddQ,
   dddW genes) lyse
   b. MeSH (dmd genes) demethylate

Question 21

What happens to DMS?

Answer 21

1. 90% re-catabolised by marine bacteria as
   carbon source (Methylophaga spp.)
2. Other 10% transferred from marine
   system to atmosphere (~35 million
   tonnes)
   a. major biogenetic source of sulfur in
   atmosphere

Question 22

What happens to DMS in the atmosphere?

What is CNN?

Answer 22

1. DMS oxidation produces products
2. these products act as “Cloud
   Condensation Nuclei” (CNN)
3. Climate cooling effect by reflecting
   sunlight
4. AS WELL AS THIS, clouds then move, from marine to terrestrial systems, COMPLETEING GLOBAL SULFUR SYSTEMS

CNN is the ‘nucleus’ for which water droplets form around, leading to a cloud

Question 23

Explain the CLAW hypothesis

Answer 23

1. Proposition that DMSP dependent DMS 
   production as a negative mechanism by 
   which phytoplankton regulate their 
   environment in CLAW
   a. Phytoplankton prod. DMSP...
   b. If it gets too cold they make more 
       DMSP = more DMS
   c. = more DMS in atmosphere
   d. increases cloud cover
   e. BACTERIA ESSENTIALLY REGULATING 
       THE ENVIRONEMT FOR THEMSELF