Marine Microbiology

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Marine Microbiology
Marine Microbiology Module 2
1. Extent of marine environment 2. Main
distinguishing environmental features    
Salinity     Temperature     Pressure
Currents     Dissolved Gases     Chemistry and
Ionic balance (buffer systems for pH)  3. Deep
sea thermal vents and their importance 4. How
these features affect marine microbial growth and
activity
R/V Polar Duke - U.S. National Science Foundation
(NSF) flagship for science programs in the region
of the Antarctic Peninsula The penguin is lost.
WebLink
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Extent of Marine Environment

• Extent of the Marine Environment
• The marine environment is by far the largest part
  of the biosphere, being about 97-98 of all the
  water on earth.
• Approximately 75 of the ocean is below 1000 M
  depth and is constantly cold (about 3C on
  average).
• The deepest part of the oceans (in the various
  "trenches" in the sea floor) is about 11,000 M
  deep and is at a pressure of about 1000
  atmospheres. (1 atmosphere increase in pressure
  for each 10 M in depth).
• These large pressure differences lead to
  different microorganisms being present at
  different depths in the ocean. Some, the
  barophiles, can be moderate (growing best at 400
  atm but still able to grow at 1 atm) or extreme
  (growing only at higher pressures).
• Yet other bacteria are barotolerant (growing best
  at lower pressures, but able to tolerate up to
  400 atmospheres in some cases). The very high
  pressures found at depth in the sea affect many
  different biochemical and biological processes.

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Marine Environment (contd.)

• Although most research has been in the
  near-shore and estuarine marine environments,
  there is increasing interest in the off-shore and
  pelagic ocean.
• The true off-shore is where the ocean is more
  than 1000 metres deep, then 62 of the Earths
  surface is in the pelagic and deep sea region.
• In terms of volume, this is about 98 of the
  worlds oceans. Microorganisms are involved in
  most of the geochemical cycling in the oceans,
  but surprisingly little is known of the
  activities at these depths.

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Salinity
Salinity 
The composition of seawater is approximately 36
parts per thousand of salts, Their composition
is
Nitrogen and phosphorus are not major elements in
oceans, but are present along with almost every
other element in sufficient quantity for
biological activity. The pH is between 6.5 and
8.3 with an average that is slightly above pH
7.0. pH values rarely have an effect on
availability of ions and elements except for the
CO3- and HCO3- system
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Borate Buffer
The borate buffer system
This buffer system is inherently self-balancing
the acid production (H) releases the Ca and
CO3 from the calcium carbonate deposited as a
precipitate as a result of the change in pH to
more alkaline conditions. There is then excess
base that reacts in the borate buffer system to
release the H
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Dissolved gases
Dissolved Gases

• Carbon dioxide input is the most important
  gaseous exchange. The total carbon dioxide
  content of the atmosphere is about 600 billion
  tons. There is at least 100 times this in
  seawater, present as carbon dioxide and carbonate
  and bicarbonate ions.
• Both carbon dioxide and bicarbonate ions are 
  utilized by plants for growth. The availability
  of the two species depends on the pH of the sea
  water.
• The equilibrium between carbon dioxide,
  carbonate and bicarbonate (above) is in favor of
  bicarbonate at pH levels near neutrality but at
  pH 9.4 carbonate is present in large quantities
  and is precipitated as carbonate by the calcium
  ions in sea water.
• Photosynthesis stops in sea water at pH 9.4 even
  in bright light, due to this precipitation. In
  fresh water, due to the low calcium levels,
  photosynthesis can continue at pH levels up to
  10.1.

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Pressure
Pressure

• Pressure increases at the rate of 1 atmosphere
  for every 10 metres depth increase. In the
  deepest parts of the ocean, (at depths of 10,000
  metres) the pressure can exceed 1000 atmospheres.
  
• Many marine bacteria in the deeper regions of
  oceans are adapted to these high pressures they
  are barophilic and cannot tolerate lower
  hydrostatic pressures.
• These pressures are high enough to affect
  biochemical reactions due to size differences in
  the reactants and products most non-barophilic
  marine bacteria show an increase in biochemical
  reaction rates at pressures around 100
  atmospheres, but show a decrease in these rates
  as the pressures increase above 100 atmospheres.

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Deep Sea Vents
Deep Sea Volcanic Vents

• In the 1970s, a new community was discovered in
  the ocean. It was formed around thermal volcanic
  vents in the ocean floor and obtained its energy
  from the chemoautotrophic metabolism of the
  sulfide-rich water issuing from the vents.
• Sea water penetrates down several kilometres
  into the hot basalt layers in the Earth's crust
  around the spreading centres for the Earth's
  plates.
• Plate tectonics has shown that these plates are
  moving apart at rates of 2-15 cm per year as the
  continents move apart.
• The sea water in contact with the hot basalt may
  have a temperature of 360C (higher than 100C
  because of the pressures at these depths). It
  emerges on the sea floor as warm (8-25C) or hot
  (160-350C) water from vents.
• The sulphide content can be as high as 160 mmol
  L-1

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Diagram of Deep Sea Vents
The energy source is the aerobic and anaerobic
chemosynthetic reduction of carbon dioxide to
organic carbon using geothermally reduced
inorganic compounds as the energy source. This
chemosynthetic system is unique - it gets energy
from a terrestrial source - not from sunlight
either directly or indirectly.
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Deep Sea Vents
Hydrothermal circulation occurs when seawater
penetrates into the ocean crust, becomes heated,
reacts with the crustal rock, and rises to the
seafloor. Seafloor hydrothermal systems have a
major local impact on the chemistry of the ocean
that can be measured in hydrothermal plumes.
Some hydrothermal tracers (especially helium)
can be mapped thousands of kilometers from their
hydrothermal sources, and can be used to
understand deep ocean circulation. Because
hydrothermal circulation removes some compounds
from seawater (e.g. Mg, SO4) and adds many others
(He, Mn, Fe, H2, CO2), it is an important process
in governing the composition of seawater.
There is an enormous quantity of life surrounding
these vents, much more than could be supported by
the input of organic materials from
photosynthesis in the photic zones above. Large
mussels and vestimentiferan tube worms (a new
family Riftidae) up to 2.6 metres long and 5 cm
thick are found around the vents. Giant white
clams have been observed close to the vents.
There is also a very specific set of
invertebrate larvae, siphonophores and active
fish populations associated with the vents.
WebLink
Volcanic Vents
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Ocean Currents
Ocean Currents

• Ocean waters are constantly on the move. How
  they move influences climate and living
  conditions for plants and animals, even on land.
• Currents flow in complex patterns affected by
  wind, the water's salinity and heat content,
  bottom topography, and the earth's rotation.
• Upwelling brings cold, nutrient-rich water from
  the depths up to the surface. Earth's rotation
  and strong seasonal winds push surface water away
  from some western coasts, so water rises on the
  western edges of continents to replace it. Marine
  life thrives in these nutrient-rich waters
• A global "conveyor belt" set in motion when deep
  water forms in the North Atlantic, sinks, moves
  south, and circulates around Antarctica, and then
  moves northward to the Indian, Pacific, and
  Atlantic basins.
• It can take a thousand years for water from the
  North Atlantic to find its way into the North
  Pacific.
• Warm surface currents invariably flow from the
  tropics to the higher latitudes, driven mainly by
  atmospheric winds, as well as the earth's
  rotation.
• Western boundary currents are good examples of
  warm surface currents they are warm and fast,
  and they move from tropical to temperate
  latitudes
• Cold surface currents come from polar and
  temperate latitudes, and they tend to flow
  towards the equator. Like the warm surface
  currents, they are driven mainly by atmospheric
  forces.

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Example of Currents

• Examples of Ocean Currents
• The Gulf Stream surface current is a western
  boundary current, one of the strongest--warm,
  deep, fast, and relatively salty. It separates
  open-ocean water from coastal water.
• The California current (next slide) is an
  eastern boundary current. It is broad, slow,
  cool, and shallow. Eastern boundary currents are
  often associated with upwelling.
• The Somali current, off Africa's eastern coast,
  is unusual because it reverses direction twice a
  year. From May to September it runs north from
  November to March it runs south. As it flows
  northward, upwelling supports productive marine
  life, but productivity falls when the current
  begins to move southward.

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California Current
Satellite Oceanography Laboratory
WebLink
A satellite infrared image of the California
Current taken on 15 June 1981 at 0400 UT.
Light gray shades correspond to cold water. The
spacing of the tic marks is 100 km. Cold
upwelled water is seen on the continental shelf
and slope shown by the 300 m and 3000 m isobaths
(dashed lines). Several upwelling filaments are
present between Cape Mendocino (124 20'W 40 20'N)
and Point Conception (120 30'W 34 30'N).
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World sea levels
The Topex/Poseidon ocean current study
WebLink
WebLink
Two years of satellite-derived Dynamic Ocean
Topography data (Global Sea Level) from the
Topex/Poseidon Mission
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Characteristics of Marine Bacteria
Characteristics of Marine Bacteria

• Many marine bacteria have an absolute
  requirement for sodium, potassium and magnesium
  ions.
• Some also require chloride ions and ferric iron.
  
• Since the organic matter in the ocean is
  produced in the top 100 to 300 metres, and over
  80 of this material is metabolized before it
  sinks below the photic zone, there is little
  organic material reaching the bottom water
  layers. It is constantly metabolized as it sinks
  through the water column.
• Any remaining residual organic materials are
  usually metabolized in the topmost sediment
  layers.

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Characteristics (contd)

• Because of this low organic matter concentration
  in the deeper levels of the ocean, most bacteria
  there have evolved to exist on such low levels
  the heterotrophic bacteria in the pelagic and
  deep ocean are often oligotrophic (adapted to low
  organic matter levels) and are inhibited by high
  organic matter concentrations.
• Many are also psychrotrophic (grow at low
  temperature 0C and also above 20C) or
  psychrophilic (grow at 0C but not above 20C) due
  to the prevailing selection pressure for
  organisms surviving and growing at the normal low
  ocean temperatures.

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Key Points

• Key Points
• Extent of marine environment
• Main distinguishing environmental features  
• Salinity    
• Temperature
• Pressure
• Dissolved Gases
• Chemistry and Ionic balance (buffer systems for
  pH)
• How these features affect marine microbial
  growth and activity
• Deep sea thermal vents and their importance

End of Module 2
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Estuarine Microbiology
Module 3 Estuarine Systems
General Description An estuary has been defined
by Pritchard (1967) as "a semi-enclosed coastal
body of water, which has a free connection with
the open sea, and within which seawater is
measurably diluted with freshwater derived from
land drainage". It is an intermediate habitat
between the sea, the land and freshwaters, and is
an extremely dynamic ecosystem. They are found
where a river finally meets the sea, and the
waters are usually calm. Estuaries have been
claimed to be the most productive natural
ecosystems in the world, and provide food for a
variety of organisms. They are important in the
commercial fishing industry, as many species use
the estuary as a breeding and nursery area. The
organisms that live in the estuary must be able
to cope with the changes in salinity, temperature
and light levels
From EPA Office of Water
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Biological Functions of Estuaries
Biological Functions of Estuaries

• Waste Assimilation
• Provision of Habitat
• Provision of Food
• Spawning Breeding Area
• Human Use of Estuaries

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Function Waste Assimilation
Waste Assimilation Estuaries are places where
fine sediments are deposited. River flow contains
a large amount of fine sediments and the often
abrupt change in current flow means that these
sediments can settle out of the water column.
Other processes encourage sediments to settle
out. Chemical processes occur when fresh and salt
water meet.  These processes cause sediment and
clay particles to flocculate and precipitate out
of the water column. This is how many heavy
metals are prevented from reaching the ocean.
These potentially dangerous substances often
remain "locked" to the sediment particle and
become active again only when natural processes
release them. This occurs gradually and acts to
regulate the circulation of the metals in the
environment. It is only when unnatural human
activities disturb these sediments that problems
can occur. This is because the substances are
released in large amounts, compared to the
gradual release that occurs naturally.
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Function Habitat
Provision of Habitat An estuary is an interface
between fresh and marine habitats. This results
in a body of water that is brackish in nature.
There are some organisms that have specifically
adapted to these conditions, but most organisms
in estuaries are from either fresh or salt water
origins. The high level of nutrients in
estuaries attracts many organisms. They live in
the water body, on the water surface, within or
above the bottom sediments, or amongst floating
vegetation. The productive nature of estuaries
provides a suitable habitat and a plentiful food
supply for many plants and animals.
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Food
Provision of Food Inputs of plant material from
vegetation surrounding the estuary are broken
down by bacteria and microorganisms. Nutrients
come into the estuary with river flow and also
with the tides. These nutrients are used by many
planktonic and aquatic plants to photosynthesize
and grow. Fringing vegetation such as grasses and
mangrove species are vital to the input of
nutrients into estuarine waters. Without these,
the nutrient levels would be drastically reduced.
Despite the large amount of plant material
available for food, estuaries do not contain a
large diversity of species. This is actually a
result of the other conditions such as salinity
and temperature, which make it difficult for many
organisms to live in an estuary. However, those
that do are often present in large numbers.
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Functions Spawning and Breeding areas Human
Uses
Spawning Breeding Area Many marine species
enter estuaries at some time during their life
cycle to breed. Because of their high nutrient
level, and the relative shelter from wind and
waves, it is an ideal environment for the growth
of young. Human Use of Estuaries Estuaries,
like many other marine ecosystems, have often
been used by humans for many undesirable
purposes. To provide more space for human
settlement, they have been dredged and filled in,
with the fringing vegetation cleared. Wastes have
been dumped in them, particularly sewage, heavy
metals, hydrocarbons and stormwater, most of
which arrive via rivers.
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Productivity

• Estuaries support a high level of primary
  productivity.
• A large amount of nutrients come in with both
  the fresh and the salt water.
• There is a large amount of light in the shallow
  water the sun's rays are able to penetrate and
  provide sufficient energy for photosynthesis.
• There is a large amount of vascular plant
  material from surrounding vegetation, which adds
  nutrients.
• Mangrove swamps are often found surrounding an
  estuary, and dead leaves and branches fall into
  the water, along with plant materials already
  partly decomposed by bacteria

Mangrove Swamp
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Adaptations of Estuarine Organisms - Salinity

• Adaptations of Estuarine Organisms 
• Estuarine organisms are derived from both
  terrestrial and marine origins, but the diversity
  of organisms that may survive in an estuary is
  limited by the harsh conditions. The temperature
  and salinity vary along the length of an estuary,
  as do the light levels. There is significant
  organic accumulation in an estuary and seagrass
  beds are common.
• Salinity
• Salinity can affect an organism in different
  ways, and these effects may vary with any of the
  following factors temperature, dissolved gases,
  density and viscosity.
• These factors will affect the levels at which
  the salinity changes become harmful. Salinity
  effects may also vary during an organism's life
  cycle.
• Generally it seems that newly hatched eggs and
  reproducing adults are more prone to salinity
  stress than organisms in the intermediate stages
  of the life cycle.

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Adaptations Salinity (2)

• Responses of estuarine organisms to salinity
  vary between species.
• Active swimmers like fish can escape changes
  fairly easily. Sedentary (attached) animals
  cannot escape these changes, but most are able to
  shut themselves away inside their shells. Benthic
  creatures can often escape salinity changes by
  retreating into their burrows and digging
  themselves in deeper if necessary.
• Organisms may become severely stressed if they
  are unable to cope with salinity changes. Many
  estuarine organisms are euryhaline, meaning that
  the organism can withstand a larger range of
  salinities without becoming too sick. Other
  organisms that are restricted to the freshwater
  end (low salinities) or the marine end (high
  salinities) are called stenohaline, meaning that
  they can only tolerate a narrow range of
  salinities.
• Rare occurrences such as floods (more
  freshwater, lower salinity) and drought (less
  freshwater, higher salinity) can have dramatic
  effects on organisms, altering the salinity
  gradient within the estuary and affecting where
  organisms can live.

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Adaptations - Temperature

• Temperature
• The temperatures within an estuary can vary
  significantly during any twenty-four hour period.
  The shallowness of estuarine waters means that
  the water is subject to heating by the sun's
  rays, and cooling due to the incoming water from
  both rivers and the sea.
• At high tide, the water temperature is usually
  quite cool. Light cannot penetrate as far in
  deeper water, so the lower layers remain
  relatively cool, with only the uppermost layers
  becoming heated.
• As the tide goes out, the water is more easily
  heated all the way through. When the tide comes
  back in again, it is often rapid and the water is
  very cool.
• Estuarine organisms must be able to deal with
  the sudden temperature changes, and many are
  eurythermal, meaning they can withstand the
  highly variable temperatures of estuarine life.
• Other organisms escape much of these changes by
  burying themselves in the bottom sediments,
  although they cannot escape them altogether.

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Microbiology of Estuaries
Microbiology of Estuaries  The rapid variations
in physical and chemical properties in estuaries
lead to the establishment of unique microbial
communities. The biomass of epiphytic (on
estuarine plants) microbial communities is
extremely large and may exceed the weight of the
typical estuarine sea grasses. This epiphytic
microbial community consists of algae, diatoms
and bacteria. Because of the concentration of
nutrients in the estuary (described in Aquatic
Microbiology Module 1), the nutrient levels are
high. The biomass is therefore also high. Because
of the severe environmental fluctuations in
temperature and salinity, the microbial species
diversity is not as great as might be expected.
It is, however, greater than the species
diversity in the plants and animals in the
estuary, since bacteria are capable of existing
and growing over wider ranges of environmental
conditions.
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Microbiology (2)
As an example of this, consider the range in pH
and Eh in an estuary it is very large for both
parameters, but many of the conditions are
capable of supporting different groups of
bacteria. The graph below shows the typical
range in Eh and pH in an estuary with the
tolerance range of commonly occurring estuarine
bacterial groups superimposed. It is clear that
the range of conditions present permits a wide
range of different microbial groups (sulphur
bacteria, iron bacteria, heterotrophs, etc.) to
grow in estuaries.
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Microbiology (3)
Note the wide variation in Eh and pH in an
estuary. Also note the wide variety of organisms
that are able to colonize these niches In the
sediment conditions fluctuate less than in the
water sediment bacteria are less subject to the
rapid changes in salinity and temperature and so
are more similar to normal ocean or fresh water
sediment bacteria
Eh mv
End of Module 3
After Woods, 1965
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Microbiology (3)
Note the wide variation in Eh and pH in an
estuary. Also note the wide variety of organisms
that are able to colonize these niches In the
sediment conditions fluctuate less than in the
water sediment bacteria are less subject to the
rapid changes in salinity and temperature and so
are more similar to normal ocean or fresh water
sediment bacteria
Eh mv
End of Module 3
After Woods, 1965
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Key Points

• Key Points
• Definition of an estuary
• Environmental conditions
• Importance in ecology
• Adaptation of estuarine organisms
• Microbiology of Estuaries - why is it diverse
  and productive ?
• Range of conditions (Eh vs pH diagram) - how
  this impacts microbial activities.
• Concentration effects for nutrients in estuaries
  (from Aquatic Microbiology)

End of Module 3