BIOLOGICAL OCEANOGRAPHY

3 From shallow to deep sea environments - Distributions of the classical, major

marine systems (kelp beds, mangroves, seagrasses, coral reefs and sediments)
4, 5 How to sample the oceans. Definition of basic terms (plankton, pelagic etc.).
Introduction to the major groups of organisms, particularly phytoplankton, in the
marine food web. The Microbial Loop. Primary production. What limits
photosynthesis in the sea?
6 Photosynthetic picoplankton - Discovery, physiology, adaptation to light climate,
seasonal cycles, differences in pigment composition between the genera
Synechococcus and Prochlorococcus
7 Biogeochemical cycles. The role of micro-organisms in the cycling of carbon,
nitrogen, phosphorus and sulphur
8 Nitrogen fixation in the sea; Microbiology of hydrothermal vent communities and
adaptation to living at depth
9 Marine microbial interactions - From single cells to streamlined genomes and
microbial interdependence; ecological theories (red vs black queen); positive and
negative interactions, viral lysis and grazing.
10 Molecular approaches to assessing genetic diversity in the marine environment;
the 'great plate count anomaly'; 16S rRNA analysis; PCR approaches.
11 Anthropogenic effects on the oceans – increasing atmospheric CO 2 and the
buffering effect of the oceans, ocean acidification, eutrophication and harmful
blooms.
Nitrogen fixation in the sea
 
The ocean environment is nutrient poor – productivity relies on fluxes
and cycling of the elements composing biological material - in particular
concentrations of major nutrients: N, P, & Fe
 

Nitrogen
 

N cycle includes a gaseous phase (N2) which is fixed into biologically

available ammonium by nitrogen fixation (New production)
 
- so the atmosphere provides a large potential reservoir of N for
productivity in the marine environment
 
However, generally N2 fixation rates are low and there are few N2-
fixing organisms.
 
Why?
 
Trichodesmium, a cyanobacterium common to tropical and subtropical
waters is present in relatively high abundance and fixes nitrogen – so
what makes Trichodesmium a dominant N2-fixer?
N2-fixing apparatus nitrogenase
N2 + energy + reductant  2NH3
15 mols of ATP 6-8 electrons
per molecule of N2 fixed
- in freshwater sysytems nitrogenase is found in a wide variety of
microorganisms e.g photosynthetic bacteria ( Rhodobacter sp.), heterotrophs
(Azotobacter sp.), & cyanobacteria; These all require O2 protection of of the
enzyme.
- in cyanobacteria nitrogenase is usually found in heterocysts (specialised cells,
lacking PSII activity & hence anaerobic); or temporal separation of N2-fixation
& photosynthesis
N2-fixation genes are dispersed throughout the prokaryotic kingdom. This
suggests that N2-fixation would be expected to occur in virtually any habitat
Factors that might limit the genetic potential & expression of N 2-fixation in
the marine environment :-
i) the large energy & reductant requirement
ii) sensitivity of nitrogenase to inactivation by O 2
iii) repression of nitrogenase activity by fixed nitrogen e.g nitrate, ammonia
iv) the requirement for micronutrients such as molybdenum, vanadium & iron
Factors differ for different types of organism:
- for heterotrophs : organic C substrate availability, presence of reduced
microzones & turbulence
Is Trichodesmium the only free-living N2-fixer in oligotrophic open oceans?
 
Trichodesmium is the dominant N2-fixing organism
 
BUT Less abundant N2-fixing organisms are found in certain regions:
 
Heterocystous cyanobacterial symbionts (e.g. Richelia sp.) of certain species of
diatoms (Rhizosolenia sp. & Hemiaulus sp.) – primarily found in warm tropical and
sub-tropical waters particularly in the Pacific
 
  
 
 
 
 
 
 
 
 
 
(N.B. Blooms of Nodularia, Aphanizomenon & Anabaena in the Baltic Sea, & rich
flora of cyanobacterial & heterotrophic N2-fixing organisms in benthic mats,
coral reefs and sediments)
What is
Trichodesmium?
 
- a cyanobacterium
of the order
Oscillatoriales
 
- produce only
vegetative cells
 
- Trichodesmium
means a bundle of
threads
 
- a number of
species have been
described
 
- surface
aggregations can
be detected from
space
Is Trichodesmium a free-living organism?
 
A no. of prokaryotic and eukaryotic organisms have
been reported to be present in Trichodesmium colonies
e.g. bacteria, fungi, diatoms
 
- their exact role is unclear but likely that C and N exchanges occur between
organisms; = possibility of symbiotic or consortial interactions, or that they
play a role in the decomposition of Trichodesmium filaments
 
Is the N2-fixation apparatus of Trichodesmium particularly well adapted to
the open ocean environment?
 
- nifH gene sequence is not closely related to other cyanobacterial sequences –
this might have biochemical or physiological implications
 
BUT
 

Trichodesmium only fixes N2 during the day! – and in fact N2-fixation is light-
dependent (maximal expression is at noon – when photosynthesis is most active)
 
- odd since non-heterocystous cyanobacteria fix N 2 microaerophilically or
during the night
Trichodesmium

Maximal
nitrogenase
expression is at
noon
Diel cycle of nitrogen fixation
Possible that the cycle of nitrogen fixation is due to a circadian rhythm
(characterised by the persistence of daily rhythmic outputs under constant
conditions e.g. continuous light or darkness)
- advantage of fixing N2 during the day is that N2-fixation can be coupled to the
ATP & reductant generated by photosynthesis
- but this is offset by the physiological cost of protecting nitrogenase from O 2
inactivation (perhaps achieved by high respiration rates, or more probably a variety
of intracellular biochemical mechanisms).
Diel cycle of N2-fixation is correlated with a change in the molecular mass of
the Fe protein of nitrogenase
at night - present as a high molecular mass form (inactive)
- timing of inactivation is determined to some extent by how much N 2-fixed during
the day
light causes initiation of synthesis & return of the Fe protein to the active low
molecular mass form
modification to the inactive form also takes place in the presence of O 2
(mechanism of modification not known)
modification/demodification of the Fe protein may play a role in protection of
nitrogenase from inactivation by O2 under certain conditions
but does not explain simultaneous photosynthesis & N -fixation
Modification/demodification of the Fe protein of nitrogenase
Characteristics of Trichodesmium that may be relevant to its
planktonic existence

i) forms colonies which may

- allow self-shading to reduce photoinhibition
-provide a habitat for associated bacteria that may play a symbiotic
role or consume O2
- facilitate the creation of reduced O2 zones
 

ii) produces gas vacuoles which

-allows modification of sinking or flotation rates to maintain its
position in the water column
-allows active migration of organisms & may enhance the availability of
dilute nutrients such as P (which may ultimately control their
abundance) e.g Trichodesmium P-transport model
 

iii) extensive methylation of Trichodesmium DNA

- particularly modification of adenine residues
-may play a role in inhibition of infection of Trichodesmium by
cyanophage
-also may be important in conferring stability against high UV
irradiances in surface waters
Deep Sea Microbiology
 
Considerable biological activity is found in the photic zone (down to ca 300m)
and at depths down to 1000m (organotrophic microorganisms). Depths > 1000m
(deep sea) are in comparison ‘deserts’ and biologically inactive
Exceptions do exist though e.g hydrothermal vents
 
Living in the deep sea: 3 major environmental extremes must be overcome :
low temperature, high pressure and low nutrient levels
Below depths of 100m seawater is a constant 2-3C (bacteria are psycrophilic)
Pressure increases 1 atm for every 10m depth

Do bacteria tolerate these depths or are they adapted specifically for them?
 
Pure cultures of bacteria isolated down to ~ 4000m are barotolerant – higher
growth rates at 1 atm than 400 atm
 
Cultures obtained from ca 5000m are mildly barophilic – growng optimally at
pressures of ~400 atm but still able to grow at 1 atm
 

Samples from ca 10,000 m yield extreme (obligate) barophiles – 1 strain grew

optimally at 700-800 atm and nearly as well at 1035 atm (the pressure it
experienced in its natural environment) but would not grow at pressures below
500 atm
Hydrothermal vents
 
- thermal springs in deep water at regions in the ocean floor where hot
basalt & magma cause the floor to slowly drift apart. Seawater seeping
into cracked regions mixes with hot minerals & is emitted
 
hot vents ‘black smokers’ - hot hydrothermal fluid containing abundant
metal sulphides reaches the sea floor directly & precipitates on
emerging into cold seawater forming a tower or chimney
-fluid is emitted at 270-380C at ~ 1-2 m/sec

warm vents - where hot hydrothermal fluid is cooled by seawater

permeating the sediment
- fluid is emitted at 6-23C at 0.5 - 2 cm/sec

‘white smokers’ emit lighter-hued minerals, such as those containing

barium, calcium, and silicon. These vents also tend to have lower
temperature plumes. These are alkaline hydrothermal vents
plume
vent fluid

chimney
Around hydrothermal vents thriving invertebrate communities
exist, supported by the activity of microorganisms:
 
- tubeworms over 2m in length, & large numbers of clams & mussels
 
Considering most other locations in the deep sea are biologically
unproductive how are the animal communities around hydrothermal
vents fuelled in the absence of phototrophic primary producers?
 
- vents do not discharge organic matter
 
- rather, reduced inorganic material e.g. H2S, Mn2+, H2 & CO
 
- animal communities are dependent on lithotrophic bacteria which
grow at the expense of inorganic energy sources & CO2 & HCO3-
 
(doubtful whether bacteria actually live in the hot hydrothermal fluid
- but evidence of thermophilic bacteria of various types present in
the seawater/hydrothermal fluid gradient - at temperatures of 120-
150C)
Micro-organisms present in hydrothermal vents
 
Sulphur-oxidising lithotrophs e.g Thiobacillus, Thiomicrospira &
Beggiatoa (-subdivision of the purple-sulphur bacteria)
 
fix CO2 by the Calvin cycle
 
oxidise H2S & S2O32-  SO42- + ATP
 
Nitrifying bacteria
 
Hydrogen-oxidising bacteria
 
Iron & manganese oxidising bacteria
 
Methylotrophic bacteria (growing on methane & CO emitted from the
vents)
 
microbes thus use inorganic material to gain energy (& fix CO2)
Direct symbiotic relationships of bacteria & animals
Certain lithotrophs live symbiotically with animals of the hydrothermal vents
e.g. 2 m long tubeworms (Family Pogonophora). These lack a mouth, gut or anus
but contain a modified gastrointestinal tract consisiting of spongy tissue called
the trophosome. Trophosome tissue contains S granules, but with large numbers
~ 109 cells/g tissue of the S-oxidising bacterium Thiovulum sp.
Thiovulum produces an enzyme rhodanese catalysing : H2S & S2O32-
(thiosulphate) SO32- (sulphite) + ATP. The organism also fixes CO 2 into cellular
material.
Tubeworms are organotrophs - living off the excretory products & dead cells of
the lithotrophic symbiont. The bright red plume of the worm is rich in blood
vessels (containing unusual haemoglobins capable of preventing H 2S from
poisoning the worm)
S-oxidising bacterial communities have also been found in the gill tissues of giant
clams & mussels 
It’s possible methane-oxidising bacteria also play a role as symbionts in
hydrothermal vent animals 
Other lithotrophs (Fe & Mn oxidisers) exist as free-living bacteria growing at
the expense of reduced substances emitted from the vents - probably
contribute to 1 productivity of the ecosystem by providing food for fish which
are frequently observed around vents
Ridgeia piscesae

Bathymodiolus azoricus

Rimicaris exoculata
Alviniconcha hessleri

Riftia pachytyla
galatheid crabs
Kiwa ESR sp. nov.

Kiwa hirsuta “Yeti crab”

MacPherson 2005
(South Pacific ridge)
epibiotic bacteria associated
with East Scotia Ridge
galatheid (see Env. Micro. 10:
2623-34 (2008).